diff --git a/pkgdown.yml b/pkgdown.yml
index d3ca9636..22ec1c3a 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,7 +6,7 @@ articles:
   report_structure: report_structure.html
   tcga_projects_summary: tcga_projects_summary.html
   workflow: workflow.html
-last_built: 2023-07-19T03:33Z
+last_built: 2023-07-19T09:03Z
 urls:
   reference: https://umccr.github.io/rnasum/reference
   article: https://umccr.github.io/rnasum/articles
diff --git a/reference/arriba_pdf_read.html b/reference/arriba_pdf_read.html
index b666de93..08cd9e0b 100644
--- a/reference/arriba_pdf_read.html
+++ b/reference/arriba_pdf_read.html
@@ -94,10 +94,10 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 2</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   nm                                                                 png        </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                                                              <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> EP300.AS1__XRCC6_chr22.41195482_chr22.41636113                     /tmp/Rtmp0…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> LAPTM4A__AC098828.3_chr2.20051410_chr2.20064511                    /tmp/Rtmp0…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> FNIP1__AC112492.1.83716..DCAF8L1.218._chr5.131642783_chrX.27977775 /tmp/Rtmp0…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> ZFP64__MORC2_chr20.52096811_chr22.30963497                         /tmp/Rtmp0…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> EP300.AS1__XRCC6_chr22.41195482_chr22.41636113                     /tmp/RtmpF…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> LAPTM4A__AC098828.3_chr2.20051410_chr2.20064511                    /tmp/RtmpF…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> FNIP1__AC112492.1.83716..DCAF8L1.218._chr5.131642783_chrX.27977775 /tmp/RtmpF…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> ZFP64__MORC2_chr20.52096811_chr22.30963497                         /tmp/RtmpF…</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/search.json b/search.json
index 9b68379d..e7f99e01 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://umccr.github.io/rnasum/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 RNAsum authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://umccr.github.io/rnasum/articles/development.html","id":"ref_dataset-list","dir":"Articles","previous_headings":"","what":"ref_dataset.list","title":"Development","text":"Processed data following elements:","code":""},{"path":"https://umccr.github.io/rnasum/articles/development.html","id":"ref_genes-list","dir":"Articles","previous_headings":"","what":"ref_genes.list","title":"Development","text":"Genes interest following gene sets:","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"input-data","dir":"Articles","previous_headings":"","what":"Input data","title":"RNAsum Sections","text":"Summary input data","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"clinical-information","dir":"Articles","previous_headings":"","what":"Clinical information","title":"RNAsum Sections","text":"Treatment regimen information patient clinical information available. NOTE: confidentiality reasons, timeline (x-axis) projecting patient’s treatment regimens (y-axis) set start 1st January 2000, treatments lengths preserved.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"findings-summary","dir":"Articles","previous_headings":"","what":"Findings summary","title":"RNAsum Sections","text":"Plot table summarising altered genes listed across various report sections","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"mutated-genes","dir":"Articles","previous_headings":"","what":"Mutated genes","title":"RNAsum Sections","text":"mRNA expression levels mutated genes (containing single nucleotide variants (SNVs) insertions/deletions (indels)) measured patient’s sample average mRNA expression samples cancer patients (TCGA). section available samples available umccrise results.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"fusion-genes","dir":"Articles","previous_headings":"","what":"Fusion genes","title":"RNAsum Sections","text":"Prioritised fusion genes based arriba results annotated FusionGDB database. WGS results umccrise available fusion genes Fusion genes report section ordered based evidence genome-based data. information gene fusions methods detection visualisation can found fusions dir.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"prioritisation","dir":"Articles","previous_headings":"Fusion genes","what":"Prioritisation","title":"RNAsum Sections","text":"Fusion genes detected transcriptome data prioritised based criteria ranked following order: Involvement fusion gene(s) detected genomic data (Structural variants results available) Detected transcriptome data arriba Reported fusion event according FusionGDB database Decreasing number split reads Decreasing number pair reads Involvement cancer gene(s) (see Cancer genes section)","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"filtering","dir":"Articles","previous_headings":"Fusion genes","what":"Filtering","title":"RNAsum Sections","text":"Fusion genes detected transcriptome data reported least one following criteria met: Involvement fusion gene(s) detected genomic data (SV results available) Reported fusion event according FusionGDB database Involvement cancer gene(s) (see Cancer genes section) Split reads > 1 Pair reads > 1 split reads > 1","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"structural-variants","dir":"Articles","previous_headings":"","what":"Structural variants","title":"RNAsum Sections","text":"Similar Mutated genes analysis limited genes located within SVs detected Manta using genomic data. section available samples available Manta results.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"cn-altered-genes","dir":"Articles","previous_headings":"","what":"CN altered genes","title":"RNAsum Sections","text":"Section overlaying mRNA expression data cancer genes per-gene somatic copy-number (CN) data (PURPLE) mutation status, available.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"immune-markers","dir":"Articles","previous_headings":"","what":"Immune markers","title":"RNAsum Sections","text":"Similar Mutated genes analysis limited genes considered immune markers. immune markers used report listed PanelApp panel Immune markers WTS report.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"hrd-genes","dir":"Articles","previous_headings":"","what":"HRD genes","title":"RNAsum Sections","text":"Similar Mutated genes analysis limited genes considered homologous recombination deficiency (HRD) genes. HRD genes used report listed PanelApp panel Homologous recombination deficiency (HDR) WTS report.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"cancer-genes","dir":"Articles","previous_headings":"","what":"Cancer genes","title":"RNAsum Sections","text":"Similar analysis , limited UMCCR cancer genes.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"drug-matching","dir":"Articles","previous_headings":"","what":"Drug matching","title":"RNAsum Sections","text":"List drugs targeting variants detected mutated genes, fusion genes, structural variants-affected genes, CN altered genes, HRD genes dysregulated cancer genes, can considered treatment decision making process. Note section displayed default. Set --drugs argument TRUE present report.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"addendum","dir":"Articles","previous_headings":"","what":"Addendum","title":"RNAsum Sections","text":"Additional information, including Parameters, Reporter details R Session information, added end report.","code":""},{"path":"https://umccr.github.io/rnasum/articles/tcga_projects_summary.html","id":"primary-datasets","dir":"Articles","previous_headings":"","what":"Primary datasets","title":"TCGA Projects","text":"table summarises TCGA expression data available 33 cancer types. NOTE: reduce data processing time size final RNAsum HTML report, following datasets restricted include expression data 300 patients: BRCA, THCA, HNSC, LGG, KIRC, LUSC, LUAD, PRAD, STAD LIHC.","code":""},{"path":"https://umccr.github.io/rnasum/articles/tcga_projects_summary.html","id":"extended-datasets","dir":"Articles","previous_headings":"","what":"Extended datasets","title":"TCGA Projects","text":"extended sets available BLCA, PAAD, LUAD cohorts, including neuroendocrine tumours (NETs), intraductal papillary mucinous neoplasm (IPMNs), acinar cell carcinoma (ACC) samples large-cell neuroendocrine carcinoma (LCNEC).","code":""},{"path":"https://umccr.github.io/rnasum/articles/tcga_projects_summary.html","id":"pan-cancer-dataset","dir":"Articles","previous_headings":"","what":"Pan-Cancer dataset","title":"TCGA Projects","text":"10 samples 33 datasets combined create Pan-Cancer dataset. * Tissue codes: ** dataset cleaned based quality metrics provided Merged Sample Quality Annotations file (TSV available ), linked TCGA PanCanAtlas initiative webpage (see TCGA-data-harmonization repository details, including sample inclusion criteria).","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"data-collection","dir":"Articles","previous_headings":"","what":"1. Data collection","title":"Workflow Details","text":"Read counts data patient collected DRAGEN RNA bcbio-nextgen RNA-seq pipeline.","code":""},{"path":[]},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"counts-processing","dir":"Articles","previous_headings":"2. Data processing","what":"Counts processing","title":"Workflow Details","text":"read count data (e.g. abundance.tsv quant.sf quantification files kallisto salmon, respectively) processed according steps illustrated described . Figure 1 Counts processing scheme.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"data-collection---fig1a","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Data collection - Fig1A","title":"Workflow Details","text":"patient sample external reference cohort UMCCR internal reference set -house pancreatic cancer samples","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"transformation---fig1b","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Transformation - Fig1B","title":"Workflow Details","text":"Subset datasets include common genes Combine patient sample internal reference dataset sample + internal reference set external reference set","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"filtering-optional---fig1c","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Filtering (optional) - Fig1C","title":"Workflow Details","text":"sample + internal reference set external reference set","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"normalisation-optional---fig1d","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Normalisation (optional) - Fig1D","title":"Workflow Details","text":"sample + internal reference set external reference set","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"combination---fig1e","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Combination - Fig1E","title":"Workflow Details","text":"Subset datasets include common genes Combine sample + internal reference set external reference set","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"batch-effects-correction-optional---fig1f","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Batch-effects correction (optional) - Fig1F","title":"Workflow Details","text":"Consider patient sample + internal reference (regardless patient sample origin) one batch (sets processed pipeline) corresponding TCGA dataset another batch. objective remove data variation due technical factors.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"data-scaling","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Data scaling","title":"Workflow Details","text":"processed count data scaled facilitate interpretation expression values. data either scaled: - gene-wise (Z-score transformation, default) - group-wise (centering).","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"gene-wise","dir":"Articles","previous_headings":"2. Data processing > Counts processing > Data scaling","what":"Gene-wise","title":"Workflow Details","text":"Z-scores comparable measuring observations multiples standard deviation given sample. gene-wise Z-score transformation procedure illustrated described . Figure 2 Gene-wise Z-score transformation scheme.  Extract expression values across samples given gene (Fig2A) Compute Z-scores individual samples (see equation Fig2B) internal reference set* external reference set Present patient sample Z-score context reference cohorts’ median Z-scores (Fig2D). * used pancreatic cancer patients","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"group-wise","dir":"Articles","previous_headings":"2. Data processing > Counts processing > Data scaling","what":"Group-wise","title":"Workflow Details","text":"group-wise centering apporach illustrated described . Figure 3 Group-wise centering scheme.  patient sample internal reference set* external reference set internal reference set* external reference set Center median expression values gene individual groups (Fig3C). Present patient sample centered expression values context reference cohorts’ centered values (Fig3D). * used pancreatic cancer patients","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"integration-with-wgs-based-results","dir":"Articles","previous_headings":"","what":"3. Integration with WGS-based results","title":"Workflow Details","text":"patients available WGS data processed using umccrise pipeline, expression level information mutated genes genes located within detected SVs/CNVs, well genome-based findings, incorporated used primary source expression profile prioritisation.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"somatic-snvs-and-small-indels","dir":"Articles","previous_headings":"3. Integration with WGS-based results","what":"Somatic SNVs and small indels","title":"Workflow Details","text":"Check PCGR tiered TSV output file available (e.g. ). Extract expression level information genome-based findings genes detected genomic variants (use --pcgr_tier argument define tier threshold value). Order genes increasing variant tier decreasing absolute values representing difference expression levels patient sample corresponding reference cohort.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"structural-variants","dir":"Articles","previous_headings":"3. Integration with WGS-based results","what":"Structural variants","title":"Workflow Details","text":"Check Manta annotated TSV output file available (e.g. example input). Extract expression level information genome-based findings genes located within detected SVs Order genes increasing SV score decreasing absolute values representing difference expression levels patient sample corresponding reference cohort. Compare gene fusions detected WTS data (arriba pizzly) WGS data (Manta) Prioritise WGS-supported gene fusions.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"somatic-cnvs","dir":"Articles","previous_headings":"3. Integration with WGS-based results","what":"Somatic CNVs","title":"Workflow Details","text":"Check PURPLE output file available (e.g. example input). Extract expression level information genome-based findings genes located within detected CNVs (use --cn_loss --cn_gain arguments define CN threshold values classify genes within lost gained regions). Order genes increasing (genes within lost regions) decreasing (genes within gained regions) Copy Number decreasing absolute values representing difference expression levels patient sample corresponding reference cohort.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"results-annotation","dir":"Articles","previous_headings":"","what":"4. Results annotation","title":"Workflow Details","text":"WTS- /WGS-based results altered genes collated knowledge derived -house resources public databases (listed ), provide additional sources evidence significance, e.g. flag variants clinical significance potential druggable targets.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"key-cancer-genes","dir":"Articles","previous_headings":"4. Results annotation","what":"Key cancer genes","title":"Workflow Details","text":"UMCCR cancer gene panel builds several sources: Cancermine least 2 publications least 3 citations NCG known cancer genes Tier 1 COSMIC Cancer Gene Census (CGC) CACAO hotspot genes (curated ClinVar, CiViC, Cancer Hotspots) Cancer predisposition genes (CPSR list) COSMIC Cancer Gene Census (tier 2) AstraZeneca 300 (AZ300) Familial Cancer OncoKB annotated MSKC-IMPACT MSKC-Heme PMCC-CCP Illumina-TS500 TEMPUS Foundation One Foundation Heme Vogelstein Used extracting expression levels cancer genes (presented Cancer genes report section) Used prioritise candidate fusion genes","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"oncokb","dir":"Articles","previous_headings":"4. Results annotation","what":"OncoKB","title":"Workflow Details","text":"OncoKB gene list used annotate altered genes across various sections report (annotations URL links External resources column report Summary tables).","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"vicc","dir":"Articles","previous_headings":"4. Results annotation","what":"VICC","title":"Workflow Details","text":"Variant Interpretation Cancer Consortium (VICC) knowledgebase used annotate altered genes across various sections report (annotations URL links External resources column report Summary tables).","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"civic","dir":"Articles","previous_headings":"4. Results annotation","what":"CIViC","title":"Workflow Details","text":"Clinical Interpretation Variants Cancer (CIViC) database used annotate altered genes across various sections report (annotations URL links External resources column report Summary tables). Used flag clinically actionable aberrations Drug matching report section.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"cgi","dir":"Articles","previous_headings":"4. Results annotation","what":"CGI","title":"Workflow Details","text":"Cancer Genome Interpreter (CGI) database used flag genes known involved gene fusions prioritise candidate fusion genes.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"fusiongdb","dir":"Articles","previous_headings":"4. Results annotation","what":"FusionGDB","title":"Workflow Details","text":"FusionGDB database used flag genes known involved gene fusions prioritise candidate gene fusions.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"report-generation","dir":"Articles","previous_headings":"4. Results annotation","what":"5. Report generation","title":"Workflow Details","text":"final RNAsum HTML Patient Transcriptome Summary report contains searchable tables interactive plots presenting expression levels altered genes, well links public resources providing additional source evidence significance.","code":""},{"path":"https://umccr.github.io/rnasum/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sehrish Kanwal. Author, maintainer. Jacek Marzec. Author.","code":""},{"path":"https://umccr.github.io/rnasum/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kanwal S, Marzec J (2023). RNAsum: Robust Tool Performing Transcriptome Profiling Cancer Data. https://umccr.github.io/RNAsum/, https://github.com/umccr/RNAsum.","code":"@Manual{,   title = {RNAsum: A Robust Tool for Performing Transcriptome Profiling on Cancer Data},   author = {Sehrish Kanwal and Jacek Marzec},   year = {2023},   note = {https://umccr.github.io/RNAsum/, https://github.com/umccr/RNAsum}, }"},{"path":"https://umccr.github.io/rnasum/index.html","id":"rnasum","dir":"","previous_headings":"","what":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"RNAsum R package can post-process, summarise visualise outputs primarily DRAGEN RNA pipelines. main application complement genome-based findings umccrise pipeline provide additional evidence detected alterations. DOCS: https://umccr.github.io/RNAsum","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"R package can installed directly GitHub source: Conda package available Anaconda umccr channel: Docker image available GitHub Container Registy:","code":"remotes::install_github(\"umccr/RNAsum\") # latest master commit remotes::install_github(\"umccr/RNAsum@v0.0.X\") # version 0.0.X remotes::install_github(\"umccr/RNAsum@abcde\") # commit abcde remotes::install_github(\"umccr/RNAsum#123\") # PR 123 conda install r-rnasum==0.0.X -c umccr -c conda-forge -c bioconda docker pull ghcr.io/umccr/rnasum:latest"},{"path":"https://umccr.github.io/rnasum/index.html","id":"workflow","dir":"","previous_headings":"","what":"Workflow","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"pipeline consists five main components illustrated briefly described . details, see workflow.md.  Collect patient WTS data DRAGEN RNA pipeline including per-gene read counts gene fusions. Add expression data reference cohorts get idea expression levels genes interest cancer patient cohorts. read counts normalised, transformed converted scale allows present patient’s expression measurements context reference cohorts. Supply genome-based findings whole-genome sequencing (WGS) data focus genes interest provide additional evidence dysregulation mutated genes, genes located within detected structural variants (SVs) copy-number (CN) altered regions. RNAsum designed compatible WGS patient outputs generated umccrise. Collate results knowledge derived -house resources public databases provide additional sources evidence clinical significance altered genes e.g. flag variants clinical significance potential druggable targets. final product interactive HTML report searchable tables plots presenting expression levels genes interest. report consists several sections described .","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"reference-data","dir":"","previous_headings":"","what":"Reference data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"reference expression data available 33 cancer types derived external (TCGA) internal (UMCCR) resources.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"external-reference-cohorts","dir":"","previous_headings":"Reference data","what":"External reference cohorts","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"order explore expression changes patient, built high-quality pancreatic cancer reference cohort. Depending tissue patient’s sample taken, one 33 cancer datasets TCGA can used reference cohort comparing expression changes genes interest patient. Additionally, 10 samples 33 TCGA datasets combined create Pan-Cancer dataset, cohorts extended sets also available. available datasets listed TCGA projects summary table. datasets processed using methods described TCGA-data-harmonization repository. dataset interest can specified using one TCGA project IDs RNAsum --dataset argument (see Examples).","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"internal-reference-cohort","dir":"","previous_headings":"Reference data","what":"Internal reference cohort","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"publicly available TCGA datasets expected demonstrate prominent batch effects compared -house WTS data due differences applied experimental procedures analytical pipelines. Moreover, TCGA data may include samples tissue material lower quality cellularity compared samples processed using local protocols. address issues, built high-quality internal reference cohort processed using pipelines input data (see data pre-processing). internal reference set 40 pancreatic cancer samples based WTS data generated UMCCR processed bcbio-nextgen RNA-seq pipeline minimise potential batch effects investigated samples reference cohort make sure data comparable. internal reference cohort assembly summarised Pancreatic-data-harmonization repository. Note two rationales using internal reference cohort: batch effects correction reference point comparing per-gene expression levels observed data patient interest data pancreatic cancer patients. case samples cancer type data internal reference cohort used batch effects correction procedure performed minimise technical-related variation data.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"input-data","dir":"","previous_headings":"","what":"Input data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"RNAsum accepts WTS data processed DRAGEN RNA pipeline. Additionally, WTS data can integrated WGS-based data processed using umccrise pipeline. latter case, genome-based findings corresponding patient sample incorporated report used primary source expression profile prioritisation.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"wts","dir":"","previous_headings":"Input data","what":"WTS","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"required WTS input data read counts provided quantification file DRAGEN RNA pipeline.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"dragen-rna","dir":"","previous_headings":"Input data > WTS","what":"DRAGEN RNA","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"table lists input data accepted RNAsum: files expected organised following structure:","code":"| |____<SampleName>   |____<SampleName>quant.sf   |____<SampleName>.fusion_candidates.final"},{"path":"https://umccr.github.io/rnasum/index.html","id":"wgs","dir":"","previous_headings":"Input data","what":"WGS","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"RNAsum designed compatible WGS outputs generated umccrise. table lists input data accepted RNAsum: files expected organised following structure:","code":"| |____umccrised   |____<SampleName>     |____pcgr     | |____<SampleName>-somatic.pcgr.snvs_indels.tiers.tsv     |____purple     | |____<SampleName>.purple.gene.cnv     |____structural       |____<SampleName>-manta.tsv"},{"path":"https://umccr.github.io/rnasum/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"Note Human reference genome GRCh38 (Ensembl based annotation version 86) used gene annotation default. GRCh37 longer supported.","code":"rnasum_cli=$(Rscript -e 'x = system.file(\"cli\", package = \"RNAsum\"); cat(x, \"\\n\")' | xargs) export PATH=\"${rnasum_cli}:${PATH}\" $ rnasum.R --version rnasum.R x.x.x  $ rnasum.R --help Usage =====   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RNAsum/cli/rnasum.R [options]   Options ======= --arriba_pdf=ARRIBA_PDF         File path of Arriba PDF output  --arriba_tsv=ARRIBA_TSV         File path of Arriba TSV output  --batch_rm=BATCH_RM         Remove batch-associated effects between datasets? [def: TRUE]  --cn_gain=CN_GAIN         CN threshold value to classify genes within gained regions [def: 95]  --cn_loss=CN_LOSS         CN threshold value to classify genes within lost regions [def: 5]  --dataset=DATASET         Dataset to be used as external reference cohort [def: PANCAN]  --dataset_name_incl=DATASET_NAME_INCL         Include dataset in report name? [def: FALSE]  --dragen_fusions=DRAGEN_FUSIONS         File path to DRAGEN RNA-seq 'fusion_candidates.final' output  --drugs=DRUGS         Include drug matching section in report? [def: FALSE]  --filter=FILTER         Filter out low expressed genes? [def: TRUE]  --hide_code_btn=HIDE_CODE_BTN         Hide \"Code\" button above code chunks in report? [def: TRUE]  --immunogram=IMMUNOGRAM         Include immunogram in report? [def: FALSE]  --log=LOG         Log2 transform data before normalisation? [def: TRUE]  --manta_tsv=MANTA_TSV         File path to umccrise 'manta.tsv' output  --norm=NORM         Normalisation method  --pcgr_splice_vars=PCGR_SPLICE_VARS         Include non-coding splice region variants reported in PCGR? [def: TRUE]  --pcgr_tier=PCGR_TIER         Tier threshold for reporting variants reported in PCGR [def: 4]  --pcgr_tiers_tsv=PCGR_TIERS_TSV         File path to PCGR 'snvs_indels.tiers.tsv' output  --project=PROJECT         Project name  --purple_gene_tsv=PURPLE_GENE_TSV         File path to PURPLE 'purple.cnv.gene.tsv' output  --report_dir=REPORT_DIR         Directory path to output report  --salmon=SALMON         File path to salmon 'quant.sf' output  --sample_name=SAMPLE_NAME         Sample name to be presented in report  --sample_source=SAMPLE_SOURCE         Type of investigated sample [def: -]  --save_tables=SAVE_TABLES         Save interactive summary tables as HTML? [def: TRUE]  --scaling=SCALING         Scaling for z-score transformation (gene-wise or group-wise) [def: gene-wise]  --subject_id=SUBJECT_ID         Subject ID  --top_genes=TOP_GENES         Number of top ranked genes to be presented in report  --transform=TRANSFORM         Transformation method to be used when converting read counts [def: CPM]  --umccrise=UMCCRISE         Directory path of the corresponding WGS-related data  --help, -h         Show this help message and exit"},{"path":"https://umccr.github.io/rnasum/index.html","id":"examples","dir":"","previous_headings":"Usage","what":"Examples","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"RNAsum CLI commands generating HTML reports different data availability scenarios: WTS data WTS WGS data WTS WGS clinical data Note Example data provided /inst/rawdata/test_data folder GitHub repo. RNAsum runtime less 20 minutes using 16GB RAM memory 1 CPU.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"id_1-wts-and-wgs-data","dir":"","previous_headings":"Usage > Examples","what":"1. WTS and WGS data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"frequent preferred case, WGS-based findings used primary source expression profile prioritisation. genome-based results can incorporated report specifying location corresponding umccrise output files (including results PCGR, PURPLE, Manta) using --umccrise argument. Mutated genes, Structural variants CN altered genes report sections contain information expression levels mutated genes, genes located within detected SVs CN altered regions, respectively. results Fusion genes section ordered based evidence genome-based data. subset TCGA pancreatic adenocarcinoma dataset used reference cohort (--dataset TEST). HTML report test_sample_WTS.RNAsum.html created inst/rawdata/test_data/dragen/RNAsum folder.","code":"rnasum.R \\   --sample_name test_sample_WTS \\   --dataset TEST \\   --dragen_rnaseq inst/rawdata/test_data/dragen \\   --report_dir inst/rawdata/test_data/dragen/RNAsum \\   --umccrise inst/rawdata/test_data/umccrised/test_sample_WGS \\   --save_tables FALSE"},{"path":"https://umccr.github.io/rnasum/index.html","id":"id_2-wts-data-only","dir":"","previous_headings":"Usage > Examples","what":"2. WTS data only","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"scenario, WTS data used expression levels key UMCCR Cancer genes, Fusion genes, Immune markers homologous recombination deficiency genes (HRD genes) reported. Moreover, gene fusions reported Fusion genes report section contain information evidence genome-based data. subset TCGA pancreatic adenocarcinoma dataset used reference cohort (--dataset TEST). output HTML report test_sample_WTS.RNAsum.html created inst/rawdata/test_data/dragen/RNAsum folder.","code":"rnasum.R \\   --sample_name test_sample_WTS \\   --dataset TEST \\   --dragen_rnaseq inst/rawdata/test_data/dragen \\   --report_dir inst/rawdata/test_data/dragen/RNAsum \\   --save_tables FALSE"},{"path":"https://umccr.github.io/rnasum/index.html","id":"id_3-wts-wgs-and-clinical-data","dir":"","previous_headings":"Usage > Examples","what":"3. WTS WGS and clinical data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"samples derived subjects, clinical information available, treatment regimen timeline can added HTML report. can added specifying location relevant excel spreadsheet (see example test_clinical_data.xlsx inst/rawdata/test_data/test_clinical_data.xlsx) using --clinical_info argument. spreadsheet, least one following columns expected: NEOADJUVANT REGIMEN, ADJUVANT REGIMEN, FIRST LINE REGIMEN, SECOND LINE REGIMEN THIRD LINE REGIMEN, along START STOP dates corresponding treatments. subset TCGA pancreatic adenocarcinoma dataset used reference cohort (--dataset TEST). HTML report test_sample_WTS.RNAsum.html created ../rawdata/test_data/stratus/test_sample_WTS_dragen_v3.9.3/RNAsum folder.","code":"rnasum.R \\   --sample_name test_sample_WTS \\   --dataset TEST \\   --dragen_rnaseq $(pwd)/../rawdata/test_data/dragen \\   --report_dir $(pwd)/../rawdata/test_data/dragen/RNAsum \\   --umccrise $(pwd)/../rawdata/test_data/umccrised/test_sample_WGS \\   --save_tables FALSE \\   --clinical_info $(pwd)/../rawdata/test_data/test_clinical_data.xlsx \\   --save_tables FALSE"},{"path":"https://umccr.github.io/rnasum/index.html","id":"output","dir":"","previous_headings":"Usage","what":"Output","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"pipeline generates HTML Patient Transcriptome Summary report results folder:","code":"| |____<output>   |____<SampleName>.<output>.html   |____results     |____exprTables     |____glanceExprPlots     |____..."},{"path":"https://umccr.github.io/rnasum/index.html","id":"report","dir":"","previous_headings":"Usage > Output","what":"Report","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"generated HTML report includes searchable tables interactive plots presenting expression levels altered genes, well links public resources describing genes interest. report consists several sections, including: Input data Clinical information* Findings summary Mutated genes** Fusion genes Structural variants** CN altered genes** Immune markers HRD genes Cancer genes Drug matching * clinical information available; see --clinical_info argument  ** genome-based results available; see --umccrise argument Detailed description report structure, including result prioritisation visualisation available .","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"results","dir":"","previous_headings":"Usage > Output","what":"Results","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"results folder contains intermediate files, including plots tables presented HTML report.","code":""},{"path":"https://umccr.github.io/rnasum/reference/CapStr.html","id":null,"dir":"Reference","previous_headings":"","what":"Capitalise input string — CapStr","title":"Capitalise input string — CapStr","text":"Capitalises input string.","code":""},{"path":"https://umccr.github.io/rnasum/reference/CapStr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capitalise input string — CapStr","text":"","code":"CapStr(x)"},{"path":"https://umccr.github.io/rnasum/reference/CapStr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capitalise input string — CapStr","text":"x Input string.","code":""},{"path":"https://umccr.github.io/rnasum/reference/CapStr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capitalise input string — CapStr","text":"Capitalised string.","code":""},{"path":"https://umccr.github.io/rnasum/reference/REFERENCE_DATASETS.html","id":null,"dir":"Reference","previous_headings":"","what":"RNAsum Reference Datasets — REFERENCE_DATASETS","title":"RNAsum Reference Datasets — REFERENCE_DATASETS","text":"Reference datasets available RNAsum.","code":""},{"path":"https://umccr.github.io/rnasum/reference/REFERENCE_DATASETS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RNAsum Reference Datasets — REFERENCE_DATASETS","text":"","code":"data(REFERENCE_DATASETS)"},{"path":"https://umccr.github.io/rnasum/reference/REFERENCE_DATASETS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"RNAsum Reference Datasets — REFERENCE_DATASETS","text":"list lists project abbreviation code, name, tissue code number samples 40 datasets.","code":""},{"path":"https://umccr.github.io/rnasum/reference/RNAsum-package.html","id":null,"dir":"Reference","previous_headings":"","what":"RNAsum: A Robust Tool for Performing Transcriptome Profiling on Cancer Data — RNAsum-package","title":"RNAsum: A Robust Tool for Performing Transcriptome Profiling on Cancer Data — RNAsum-package","text":"RNA-seq reporting workflow designed post-process, summarise visualise output bcbio-nextgen RNA-seq Dragen RNA pipelines. main application complement genome-based findings provide additional evidence detected alterations.","code":""},{"path":[]},{"path":"https://umccr.github.io/rnasum/reference/RNAsum-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"RNAsum: A Robust Tool for Performing Transcriptome Profiling on Cancer Data — RNAsum-package","text":"Maintainer: Sehrish Kanwal kanwals@unimelb.edu.au (ORCID) Authors: Jacek Marzec jacek.marzec@unimelb.edu.au","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Arriba PDF File — arriba_pdf_read","title":"Read Arriba PDF File — arriba_pdf_read","text":"Reads PDF output Arriba containing one fusion plot per page converts page separate PNG file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Arriba PDF File — arriba_pdf_read","text":"","code":"arriba_pdf_read(pdf = NULL, fusions = NULL, outdir = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Arriba PDF File — arriba_pdf_read","text":"pdf Output PDF file Arriba. fusions Tibble fusions Arriba. outdir Directory write output PNGs .","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Arriba PDF File — arriba_pdf_read","text":"Tibble paths created PNG images clean names. PDF (required params) NULL, returns NULL.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Arriba PDF File — arriba_pdf_read","text":"","code":"pdf <- system.file(\"rawdata/test_data/dragen/arriba/fusions.pdf\", package = \"RNAsum\") tsv <- system.file(\"rawdata/test_data/dragen/arriba/fusions.tsv\", package = \"RNAsum\") fusions <- arriba_tsv_read(tsv) (pngs <- arriba_pdf_read(pdf, fusions, tempdir())) #> # A tibble: 4 × 2 #>   nm                                                                 png         #>   <chr>                                                              <chr>       #> 1 EP300.AS1__XRCC6_chr22.41195482_chr22.41636113                     /tmp/Rtmp0… #> 2 LAPTM4A__AC098828.3_chr2.20051410_chr2.20064511                    /tmp/Rtmp0… #> 3 FNIP1__AC112492.1.83716..DCAF8L1.218._chr5.131642783_chrX.27977775 /tmp/Rtmp0… #> 4 ZFP64__MORC2_chr20.52096811_chr22.30963497                         /tmp/Rtmp0…"},{"path":"https://umccr.github.io/rnasum/reference/arriba_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process Arriba Fusions — arriba_process","title":"Process Arriba Fusions — arriba_process","text":"Process Arriba Fusions","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process Arriba Fusions — arriba_process","text":"","code":"arriba_process(arriba.fusions, known_translocations, genes_cancer)"},{"path":"https://umccr.github.io/rnasum/reference/arriba_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process Arriba Fusions — arriba_process","text":"arriba.fusions Parsed tibble Arriba fusions. known_translocations Tibble known translocations. genes_cancer Character vector cancer genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process Arriba Fusions — arriba_process","text":"Tibble post-processed Arriba fusion calls.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_summary_write.html","id":null,"dir":"Reference","previous_headings":"","what":"Write Arriba Fusion Summary — arriba_summary_write","title":"Write Arriba Fusion Summary — arriba_summary_write","text":"Writes Arriba fusion summary information (gene1__gene2_bp1_bp2).","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_summary_write.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write Arriba Fusion Summary — arriba_summary_write","text":"","code":"arriba_summary_write(x, file)"},{"path":"https://umccr.github.io/rnasum/reference/arriba_summary_write.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write Arriba Fusion Summary — arriba_summary_write","text":"x Tibble Arriba fusions NULL. file File write summary info .","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_summary_write.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write Arriba Fusion Summary — arriba_summary_write","text":"input invisibly.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Arriba TSV File — arriba_tsv_read","title":"Read Arriba TSV File — arriba_tsv_read","text":"Reads TSV file output Arriba.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Arriba TSV File — arriba_tsv_read","text":"","code":"arriba_tsv_read(x = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Arriba TSV File — arriba_tsv_read","text":"x Path Arriba TSV file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Arriba TSV File — arriba_tsv_read","text":"tibble contents input TSV file, NULL input NULL TSV data rows.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Arriba TSV File — arriba_tsv_read","text":"","code":"x <- system.file(\"rawdata/test_data/dragen/arriba/fusions.tsv\", package = \"RNAsum\") (a <- arriba_tsv_read(x)) #> # A tibble: 4 × 30 #>   gene1     gene2      `strand1(gene/fusion)` `strand2(gene/fusion)` breakpoint1 #>   <chr>     <chr>      <chr>                  <chr>                  <chr>       #> 1 EP300-AS1 XRCC6      -/-                    +/+                    chr22:4119… #> 2 LAPTM4A   AC098828.3 -/-                    -/-                    chr2:20051… #> 3 FNIP1     AC112492.… -/-                    ./+                    chr5:13164… #> 4 ZFP64     MORC2      -/-                    -/-                    chr20:5209… #> # ℹ 25 more variables: breakpoint2 <chr>, site1 <chr>, site2 <chr>, type <chr>, #> #   split_reads1 <dbl>, split_reads2 <dbl>, discordant_mates <dbl>, #> #   coverage1 <dbl>, coverage2 <dbl>, confidence <chr>, reading_frame <chr>, #> #   tags <chr>, retained_protein_domains <chr>, #> #   closest_genomic_breakpoint1 <chr>, closest_genomic_breakpoint2 <chr>, #> #   gene_id1 <chr>, gene_id2 <chr>, transcript_id1 <chr>, transcript_id2 <chr>, #> #   direction1 <chr>, direction2 <chr>, filters <chr>, …"},{"path":"https://umccr.github.io/rnasum/reference/barPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate bar-plot for selected genes — barPlot","title":"Generate bar-plot for selected genes — barPlot","text":"Generates bar-plot selected genes, highlighting samples interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/barPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate bar-plot for selected genes — barPlot","text":"","code":"barPlot(   gene,   data,   targets,   y_title = \"Counts\",   sampleName,   ext_cancer,   int_cancer,   add_cancer = NULL )"},{"path":"https://umccr.github.io/rnasum/reference/barPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate bar-plot for selected genes — barPlot","text":"gene User defined gene. data Input data. targets Targets. y_title Title y-axis. sampleName Sample name. ext_cancer External cancer group. int_cancer Internal cancer group. add_cancer Used reordering groups.","code":""},{"path":"https://umccr.github.io/rnasum/reference/barPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate bar-plot for selected genes — barPlot","text":"Bar-plot selected genes, highlighting samples interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cdfPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate CDF plot for selected gene — cdfPlot","title":"Generate CDF plot for selected gene — cdfPlot","text":"Generates cumulative distribution function (CDF) plot selected gene. option \"addBoxPlot\" = TRUE, generate additional boxplot show data variance selected gene individual groups","code":""},{"path":"https://umccr.github.io/rnasum/reference/cdfPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate CDF plot for selected gene — cdfPlot","text":"","code":"cdfPlot(   gene,   data,   targets,   sampleName,   int_cancer,   ext_cancer,   comp_cancer,   add_cancer = NULL,   addBoxPlot = FALSE,   scaling = \"gene-wise\",   report_dir )"},{"path":"https://umccr.github.io/rnasum/reference/cdfPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate CDF plot for selected gene — cdfPlot","text":"gene Gene interest. data Input data. targets Target data set. sampleName Sample name. int_cancer Internal cancer group. ext_cancer External cancer group. comp_cancer Complete cancer group. add_cancer Used reordering groups. addBoxPlot Add boc plot (boolean). scaling Gene-wise sample-wise. report_dir Output directory.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cdfPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate CDF plot for selected gene — cdfPlot","text":"Cumulative distribution function (CDF) plot selected gene.","code":""},{"path":"https://umccr.github.io/rnasum/reference/civicDrugTable.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate table with drugs targeting selected set of genes — civicDrugTable","title":"Generate table with drugs targeting selected set of genes — civicDrugTable","text":"Generates table drugs targeting selected set genes using info CIViC database (https://civicdb.org/).","code":""},{"path":"https://umccr.github.io/rnasum/reference/civicDrugTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate table with drugs targeting selected set of genes — civicDrugTable","text":"","code":"civicDrugTable(   genes,   civic_var_summaries,   civic_clin_evid,   evid_type = \"Predictive\",   var_type = NULL )"},{"path":"https://umccr.github.io/rnasum/reference/civicDrugTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate table with drugs targeting selected set of genes — civicDrugTable","text":"genes Genes interest. civic_var_summaries CIViC variant summaries. civic_clin_evid CIViC clinical evidence. evid_type Evidence type. var_type Variant type.","code":""},{"path":"https://umccr.github.io/rnasum/reference/civicDrugTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate table with drugs targeting selected set of genes — civicDrugTable","text":"Table drugs targeting selected set genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cn_subset.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy Number Subset Table — cn_subset","title":"Copy Number Subset Table — cn_subset","text":"Copy Number Subset Table","code":""},{"path":"https://umccr.github.io/rnasum/reference/cn_subset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy Number Subset Table — cn_subset","text":"","code":"cn_subset(gene.mut = NULL, cn_data, expr_data.z, expr_data.perc)"},{"path":"https://umccr.github.io/rnasum/reference/cn_subset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy Number Subset Table — cn_subset","text":"gene.mut Tibble gene alterations, PCGR run. cn_data Tibble gene MeanCopyNumber expr_data.z Tibble SYMBOL z-score expr values. expr_data.perc Tibble SYMBOL percentile expr values.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cn_subset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy Number Subset Table — cn_subset","text":"tibble Gene, CN, Diff_Perc, Diff_Z_score, Alterations PCGR run.","code":""},{"path":"https://umccr.github.io/rnasum/reference/combineDatasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine sample expression profile with reference datasets — combineDatasets","title":"Combine sample expression profile with reference datasets — combineDatasets","text":"Combines sample expression profile reference datasets. Outputs vector first element containing merged data second element containing merged targets info","code":""},{"path":"https://umccr.github.io/rnasum/reference/combineDatasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine sample expression profile with reference datasets — combineDatasets","text":"","code":"combineDatasets(sample_name, sample_counts, ref_data, report_dir)"},{"path":"https://umccr.github.io/rnasum/reference/combineDatasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine sample expression profile with reference datasets — combineDatasets","text":"sample_name Sample name. sample_counts Sample counts. ref_data Reference data. report_dir Report directory.","code":""},{"path":"https://umccr.github.io/rnasum/reference/combineDatasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine sample expression profile with reference datasets — combineDatasets","text":"Combined sample expression profile reference datasets.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cumsum_ordered.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate cumulative sum — cumsum_ordered","title":"Calculate cumulative sum — cumsum_ordered","text":"Calculating cumulative sum keeping original data order.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cumsum_ordered.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate cumulative sum — cumsum_ordered","text":"","code":"cumsum_ordered(x)"},{"path":"https://umccr.github.io/rnasum/reference/cumsum_ordered.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate cumulative sum — cumsum_ordered","text":"x Input.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cumsum_ordered.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate cumulative sum — cumsum_ordered","text":"Cumulative sum keeping order input data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/densityPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate density and expression distribution plots for selected gene — densityPlot","title":"Generate density and expression distribution plots for selected gene — densityPlot","text":"Generate density expression distribution plots selected gene, highlighting samples interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/densityPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate density and expression distribution plots for selected gene — densityPlot","text":"","code":"densityPlot(   gene,   data,   main_title,   x_title,   sampleName,   distributions = NULL,   scaling = \"gene-wise\" )"},{"path":"https://umccr.github.io/rnasum/reference/densityPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate density and expression distribution plots for selected gene — densityPlot","text":"gene Selected gene. data Input data. main_title Main title. x_title X-axis title. sampleName Sample name. distributions Distributions interest. scaling Scaling.","code":""},{"path":"https://umccr.github.io/rnasum/reference/densityPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate density and expression distribution plots for selected gene — densityPlot","text":"Density expression distribution plots selected gene.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process DRAGEN Fusions — dragen_fusions_process","title":"Process DRAGEN Fusions — dragen_fusions_process","text":"Process DRAGEN Fusions","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process DRAGEN Fusions — dragen_fusions_process","text":"","code":"dragen_fusions_process(dragen.fusions, known_translocations, genes_cancer)"},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process DRAGEN Fusions — dragen_fusions_process","text":"dragen.fusions Parsed tibble DRAGEN fusions. known_translocations Tibble known translocations. genes_cancer Character vector cancer genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process DRAGEN Fusions — dragen_fusions_process","text":"Tibble post-processed DRAGEN fusion calls.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read DRAGEN Fusions — dragen_fusions_read","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"Reads fusion_candidates.final file output DRAGEN.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"","code":"dragen_fusions_read(x = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"x Path fusion_candidates.final file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"tibble contents input TSV file, NULL input NULL TSV data rows.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"","code":"x <- system.file(\"rawdata/test_data/dragen\",   \"test_sample_WTS.fusion_candidates.final\",   package = \"RNAsum\" ) (a <- dragen_fusions_read(x)) #> # A tibble: 2 × 15 #>   gene1 gene2   Score LeftBreakpoint RightBreakpoint Gene1Location Gene2Location #>   <chr> <chr>   <dbl> <chr>          <chr>           <chr>         <chr>         #> 1 ATAD2 FBXO32  0.966 chr8:12338052… chr8:123534814… IntactExon    IntactExon    #> 2 NRIP1 AF1275… 0.658 chr21:1506474… chr21:14857708… IntactExon    IntactExon;I… #> # ℹ 8 more variables: Gene1Sense <chr>, Gene2Sense <chr>, Gene1Id <chr>, #> #   Gene2Id <chr>, NumSplitReads <dbl>, NumSoftClippedReads <dbl>, #> #   NumPairedReads <dbl>, ReadNames <chr>"},{"path":"https://umccr.github.io/rnasum/reference/empty_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Empty Tibble Given Column Names — empty_tbl","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"https://stackoverflow.com//62535671/2169986. Useful handling edge cases empty data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/empty_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"","code":"empty_tbl(cnames, ctypes = readr::cols(.default = \"c\"))"},{"path":"https://umccr.github.io/rnasum/reference/empty_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"cnames Character vector column names use. ctypes Character vector column types corresponding cnames.","code":""},{"path":"https://umccr.github.io/rnasum/reference/empty_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"tibble 0 rows given column names.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupStats_groupWise.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","title":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","text":"Calculates group-wise median, sd, quantiles cumulative fractions expression data specific sample group.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupStats_groupWise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","text":"","code":"exprGroupStats_groupWise(data, targets, target)"},{"path":"https://umccr.github.io/rnasum/reference/exprGroupStats_groupWise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","text":"data Input data. targets Target groups. target Defined biological group.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupStats_groupWise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","text":"Group-wise median, standard deviation, quantiles cumulative fractions expression data specific sample group.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupsStats_geneWise.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","title":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","text":"Calculates gene-wise median, sd, quantiles cumulative fractions expression data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupsStats_geneWise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","text":"","code":"exprGroupsStats_geneWise(data, targets)"},{"path":"https://umccr.github.io/rnasum/reference/exprGroupsStats_geneWise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","text":"data input data. targets Target groups","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupsStats_geneWise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","text":"Gene-wise median, standard deviation, quantiles cumulative fractions expression data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprTable.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate table with coloured cells indicating expression values for selected genes — exprTable","title":"Generate table with coloured cells indicating expression values for selected genes — exprTable","text":"Generates table coloured cells indicating expression values selected genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate table with coloured cells indicating expression values for selected genes — exprTable","text":"","code":"exprTable(   data = NULL,   genes = NULL,   keep_all = FALSE,   cn_data = NULL,   sv_data = NULL,   cn_decrease = TRUE,   targets,   sampleName,   int_cancer,   ext_cancer,   comp_cancer,   add_cancer = NULL,   genes_annot = NULL,   oncokb_annot = NULL,   cancer_genes = NULL,   mut_annot = NULL,   fusion_genes = NULL,   type = \"z\",   scaling = \"gene-wise\",   civic_clin_evid = NULL )"},{"path":"https://umccr.github.io/rnasum/reference/exprTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate table with coloured cells indicating expression values for selected genes — exprTable","text":"data Input data. genes Selected genes. keep_all keep rows cn_data Copy number data. sv_data SV data. cn_decrease Order CN data. targets Target groups. sampleName Sample name. int_cancer Internal cancer group. ext_cancer External cancer group. comp_cancer Complete cancer group. add_cancer Additonal cancer type. genes_annot Geners annotation. oncokb_annot OncoKb annotation. cancer_genes Cancer genes. mut_annot Mutation annotation. fusion_genes Fusion genes. type Type. scaling Scaling civic_clin_evid civic_clin_evid tibble reference genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate table with coloured cells indicating expression values for selected genes — exprTable","text":"Table coloured cells indicating expression values selected genes","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate Fusions with Ensembl Coordinates — fusions_annot","title":"Annotate Fusions with Ensembl Coordinates — fusions_annot","text":"Annotate Fusions Ensembl Coordinates","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate Fusions with Ensembl Coordinates — fusions_annot","text":"","code":"fusions_annot(fusions, gene_ann)"},{"path":"https://umccr.github.io/rnasum/reference/fusions_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate Fusions with Ensembl Coordinates — fusions_annot","text":"fusions Tibble DRAGEN Arriba fusions. gene_ann Dataframe gene annotations.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotate Fusions with Ensembl Coordinates — fusions_annot","text":"Tibble annotated genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_preprocess.html","id":null,"dir":"Reference","previous_headings":"","what":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","title":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","text":"Pre-Process Arriba DRAGEN Fusions","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_preprocess.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","text":"","code":"fusions_preprocess(d, known_translocations, genes_cancer)"},{"path":"https://umccr.github.io/rnasum/reference/fusions_preprocess.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","text":"d Parsed tibble Arriba DRAGEN fusions. known_translocations Tibble known translocations. genes_cancer Character vector cancer genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_preprocess.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","text":"Tibble post-processed fusion calls.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","title":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","text":"Get Arriba/DRAGEN Fusions Summary","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","text":"","code":"fusions_summary(tbl = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/fusions_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","text":"tbl Tibble fusions columns 'gene1' 'gene2'.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","text":"Character vector 'gene1' 'gene2' genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Fusions Table Display — fusions_table","title":"Fusions Table Display — fusions_table","text":"Fusions Table Display","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fusions Table Display — fusions_table","text":"","code":"fusions_table(fusions)"},{"path":"https://umccr.github.io/rnasum/reference/fusions_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fusions Table Display — fusions_table","text":"fusions Tibble fusions.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fusions Table Display — fusions_table","text":"DT object.","code":""},{"path":"https://umccr.github.io/rnasum/reference/genes_pcgr_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Mutated Genes from PCGR — genes_pcgr_summary","title":"Get Mutated Genes from PCGR — genes_pcgr_summary","text":"Get Mutated Genes PCGR","code":""},{"path":"https://umccr.github.io/rnasum/reference/genes_pcgr_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Mutated Genes from PCGR — genes_pcgr_summary","text":"","code":"genes_pcgr_summary(pcgr_tbl, tiers = c(1:4), splice_vars = TRUE)"},{"path":"https://umccr.github.io/rnasum/reference/genes_pcgr_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Mutated Genes from PCGR — genes_pcgr_summary","text":"pcgr_tbl Parsed PCGR TSV tibble. tiers PCGR tiers keep. Default: 1, 2, 3, 4. splice_vars Include non-coding splice region variants reported PCGR?","code":""},{"path":"https://umccr.github.io/rnasum/reference/genes_pcgr_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Mutated Genes from PCGR — genes_pcgr_summary","text":"Character vector genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/getColours.html","id":null,"dir":"Reference","previous_headings":"","what":"Assign colours to different elements — getColours","title":"Assign colours to different elements — getColours","text":"Assigns colours different elements.","code":""},{"path":"https://umccr.github.io/rnasum/reference/getColours.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Assign colours to different elements — getColours","text":"","code":"getColours(elements)"},{"path":"https://umccr.github.io/rnasum/reference/getColours.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Assign colours to different elements — getColours","text":"elements Elements interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/getColours.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Assign colours to different elements — getColours","text":"Colour assignment different elements","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Reference Data File Paths — get_refdata","title":"Get Reference Data File Paths — get_refdata","text":"Get list paths internal external reference data, based selected dataset name.","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Reference Data File Paths — get_refdata","text":"","code":"get_refdata(dataset)"},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Reference Data File Paths — get_refdata","text":"dataset Reference RNAsum dataset interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Reference Data File Paths — get_refdata","text":"List paths internal external reference datasets (Counts, Targets Name).","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Reference Data File Paths — get_refdata","text":"","code":"x <- get_refdata(dataset = \"TEST\")"},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Reference Genes — get_refgenes","title":"Get Reference Genes — get_refgenes","text":"Get list reference genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Reference Genes — get_refgenes","text":"","code":"get_refgenes(p)"},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Reference Genes — get_refgenes","text":"p RNAsum params list.","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Reference Genes — get_refgenes","text":"List tibbles corresponding cancer, oncokb, immune hrd genes","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Reference Genes — get_refgenes","text":"","code":"p <- list(   genes_cancer = system.file(\"extdata/genes/umccr_cancer_genes.2019-03-20.tsv.gz\",     package = \"RNAsum.data\"   ),   genes_oncokb = system.file(     \"extdata/OncoKB/CancerGenesList.txt.gz\",     package = \"RNAsum.data\"   ),   civic_var_summaries = system.file(     \"extdata/CIViC/01-Oct-2018-VariantSummaries.tsv.gz\",     package = \"RNAsum.data\"   ) ) x <- get_refgenes(p)"},{"path":"https://umccr.github.io/rnasum/reference/glanceExprPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","title":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","text":"Generates boxplot presenting expression profiles selected set genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/glanceExprPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","text":"","code":"glanceExprPlot(   genes,   data,   targets,   sampleName,   int_cancer,   ext_cancer,   comp_cancer,   add_cancer = NULL,   hexcode,   type = \"z\",   sort = \"diff\",   scaling = \"gene-wise\",   report_dir )"},{"path":"https://umccr.github.io/rnasum/reference/glanceExprPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","text":"genes Genes interest. data Input data. targets Target groups. sampleName Sample name. int_cancer Internal cancer group. ext_cancer External cancer group. comp_cancer Complete cancer group. add_cancer Addtional cancer type. hexcode Hexcode. type Type expression values. sort Sort order. scaling Scaling type. report_dir Reprot directory.","code":""},{"path":"https://umccr.github.io/rnasum/reference/glanceExprPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","text":"Boxplot presenting expression profiles selected set genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/immune_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Immune Gene Summary — immune_summary","title":"Get Immune Gene Summary — immune_summary","text":"Get Immune Gene Summary","code":""},{"path":"https://umccr.github.io/rnasum/reference/immune_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Immune Gene Summary — immune_summary","text":"","code":"immune_summary(tbl_imarkers, tbl_igram = NULL, igram_param = TRUE)"},{"path":"https://umccr.github.io/rnasum/reference/immune_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Immune Gene Summary — immune_summary","text":"tbl_imarkers Tibble immune response marker genes. tbl_igram Tibble immunogram genes. igram_param Immunogram inclusion TRUE/FALSE parameter.","code":""},{"path":"https://umccr.github.io/rnasum/reference/immune_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Immune Gene Summary — immune_summary","text":"Character vector genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_trans.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Known Translocations — known_trans","title":"Get Known Translocations — known_trans","text":"Flag known fusions based info : FusionGDB (https://ccsm.uth.edu/FusionGDB) Cancer Biomarkers database (CGI) (https://www.cancergenomeinterpreter.org/biomarkers)","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_trans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Known Translocations — known_trans","text":"","code":"known_trans(kt_fusiongdb, kt_cgi)"},{"path":"https://umccr.github.io/rnasum/reference/known_trans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Known Translocations — known_trans","text":"kt_fusiongdb FusionGDB parsed tibble. kt_cgi CGI parsed tibble.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_trans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Known Translocations — known_trans","text":"Tibble known translocations.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_translocations_cgi_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process CGI Known Translocations — known_translocations_cgi_process","title":"Process CGI Known Translocations — known_translocations_cgi_process","text":"Processes parsed CGI known translocations tibble, removing duplicated translocations different source.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_translocations_cgi_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process CGI Known Translocations — known_translocations_cgi_process","text":"","code":"known_translocations_cgi_process(kt_cgi)"},{"path":"https://umccr.github.io/rnasum/reference/known_translocations_cgi_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process CGI Known Translocations — known_translocations_cgi_process","text":"kt_cgi Parsed CGI tibble.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_translocations_cgi_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process CGI Known Translocations — known_translocations_cgi_process","text":"Tibble dups removed.","code":""},{"path":"https://umccr.github.io/rnasum/reference/manta_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process Manta Object — manta_process","title":"Process Manta Object — manta_process","text":"Process Manta Object","code":""},{"path":"https://umccr.github.io/rnasum/reference/manta_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process Manta Object — manta_process","text":"","code":"manta_process(manta_tsv_obj)"},{"path":"https://umccr.github.io/rnasum/reference/manta_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process Manta Object — manta_process","text":"manta_tsv_obj Manta list object read via gpgr::process_sv.","code":""},{"path":"https://umccr.github.io/rnasum/reference/manta_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process Manta Object — manta_process","text":"List : total Manta (unmelted) variants tibble melted variants genes involved multi-gene events","code":""},{"path":"https://umccr.github.io/rnasum/reference/mutCNexprPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","title":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","text":"Generates scatterplot per-gene expression values (y-axis), CN values (x-axis) mutation status info (colours), provided","code":""},{"path":"https://umccr.github.io/rnasum/reference/mutCNexprPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","text":"","code":"mutCNexprPlot(   data,   alt_data = FALSE,   cn_bottom = cn_bottom,   cn_top = cn_top,   comp_cancer,   type = \"z\",   report_dir )"},{"path":"https://umccr.github.io/rnasum/reference/mutCNexprPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","text":"data Input data. alt_data Boolean (Generates scatterplot per-gene expression values (y-axis)). cn_bottom Bottom value copy number. cn_top Top value copy number. comp_cancer Complete cancer group. type Type. report_dir Report directory.","code":""},{"path":"https://umccr.github.io/rnasum/reference/mutCNexprPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","text":"Scatterplot per-gene expression values (y-axis), CN values (x-axis) mutation status info (colours), provided.","code":""},{"path":"https://umccr.github.io/rnasum/reference/nearest_position.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for nearest value in a vector — nearest_position","title":"Check for nearest value in a vector — nearest_position","text":"Check nearest value vector.","code":""},{"path":"https://umccr.github.io/rnasum/reference/nearest_position.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for nearest value in a vector — nearest_position","text":"","code":"nearest_position(vector, x)"},{"path":"https://umccr.github.io/rnasum/reference/nearest_position.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for nearest value in a vector — nearest_position","text":"vector Input vector x Value search","code":""},{"path":"https://umccr.github.io/rnasum/reference/nearest_position.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check for nearest value in a vector — nearest_position","text":"Nearest value vector","code":""},{"path":"https://umccr.github.io/rnasum/reference/pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform PCA — pca","title":"Perform PCA — pca","text":"Perform PCA. Outputs list dataframe samples colouring info ready plotting.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform PCA — pca","text":"","code":"pca(data, targets, title = \"\", report_dir, suffix = \"\")"},{"path":"https://umccr.github.io/rnasum/reference/pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform PCA — pca","text":"data Input data. targets Target group. title Title. report_dir Report directory. suffix Suffix output file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform PCA — pca","text":"Outputs list data frame samples colouring info ready plotting.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PCGR genes with hits — pcgr_expr","title":"Get PCGR genes with hits — pcgr_expr","text":"Get PCGR genes hits","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PCGR genes with hits — pcgr_expr","text":"","code":"pcgr_expr(pcgr = NULL, expr_data.z, expr_data.perc)"},{"path":"https://umccr.github.io/rnasum/reference/pcgr_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get PCGR genes with hits — pcgr_expr","text":"pcgr Path parsed PCGR tiered TSV tibble available. expr_data.z Tibble gene symbol z-score expr values. expr_data.perc Tibble gene symbol percentile expr values.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PCGR genes with hits — pcgr_expr","text":"List.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"Reads snvs_indels.tiers.tsv file output PCGR.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"","code":"pcgr_tiers_tsv_read(x = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"x Path PCGR snvs_indels.tiers.tsv file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"tibble contents input TSV file, NULL x NULL.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"","code":"x <- system.file(   \"rawdata/test_data/umccrised/test_sample_WGS/small_variants\",   \"TEST-somatic.pcgr.snvs_indels.tiers.tsv\",   package = \"RNAsum\" ) (ptsv <- pcgr_tiers_tsv_read(x)) #> # A tibble: 99 × 61 #>    CHROM POS       REF   ALT   GENOMIC_CHANGE    GENOME_VERSION VCF_SAMPLE_ID    #>    <chr> <chr>     <chr> <chr> <chr>             <chr>          <chr>            #>  1 3     179218303 G     A     3:g.179218303G>A  grch38         SBJ02999__PRJ22… #>  2 17    7674894   G     A     17:g.7674894G>A   grch38         SBJ02999__PRJ22… #>  3 13    110715614 C     G     13:g.110715614C>G grch38         SBJ02999__PRJ22… #>  4 13    110719444 G     C     13:g.110719444G>C grch38         SBJ02999__PRJ22… #>  5 8     20250093  C     T     8:g.20250093C>T   grch38         SBJ02999__PRJ22… #>  6 8     13086457  C     T     8:g.13086457C>T   grch38         SBJ02999__PRJ22… #>  7 10    31521795  G     C     10:g.31521795G>C  grch38         SBJ02999__PRJ22… #>  8 9     132927250 G     A     9:g.132927250G>A  grch38         SBJ02999__PRJ22… #>  9 3     47121452  G     A     3:g.47121452G>A   grch38         SBJ02999__PRJ22… #> 10 6     117365075 G     C     6:g.117365075G>C  grch38         SBJ02999__PRJ22… #> # ℹ 89 more rows #> # ℹ 54 more variables: VARIANT_CLASS <chr>, SYMBOL <chr>, GENE_NAME <chr>, #> #   CCDS <chr>, CANONICAL <chr>, ENTREZ_ID <chr>, UNIPROT_ID <chr>, #> #   ENSEMBL_TRANSCRIPT_ID <chr>, ENSEMBL_GENE_ID <chr>, REFSEQ_MRNA <chr>, #> #   ONCOSCORE <chr>, ONCOGENE <chr>, TUMOR_SUPPRESSOR <chr>, #> #   ONCOGENE_EVIDENCE <chr>, TUMOR_SUPPRESSOR_EVIDENCE <chr>, #> #   DISGENET_CUI <chr>, DISGENET_TERMS <chr>, CONSEQUENCE <chr>, …"},{"path":"https://umccr.github.io/rnasum/reference/perc_rank.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","title":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","text":"Convert vector numbers corresponding vector percentiles","code":""},{"path":"https://umccr.github.io/rnasum/reference/perc_rank.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","text":"","code":"perc_rank(x)"},{"path":"https://umccr.github.io/rnasum/reference/perc_rank.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","text":"x Input vector","code":""},{"path":"https://umccr.github.io/rnasum/reference/perc_rank.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","text":"Vector percentiles","code":""},{"path":"https://umccr.github.io/rnasum/reference/prepare2write.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare object to write into a file — prepare2write","title":"Prepare object to write into a file — prepare2write","text":"Prepare object write file","code":""},{"path":"https://umccr.github.io/rnasum/reference/prepare2write.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare object to write into a file — prepare2write","text":"","code":"prepare2write(x)"},{"path":"https://umccr.github.io/rnasum/reference/prepare2write.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare object to write into a file — prepare2write","text":"x Input object.","code":""},{"path":"https://umccr.github.io/rnasum/reference/prepare2write.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare object to write into a file — prepare2write","text":"Object writing file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/purple_cnv_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PURPLE CNV Summary — purple_cnv_summary","title":"Get PURPLE CNV Summary — purple_cnv_summary","text":"Get PURPLE CNV Summary","code":""},{"path":"https://umccr.github.io/rnasum/reference/purple_cnv_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PURPLE CNV Summary — purple_cnv_summary","text":"","code":"purple_cnv_summary(tbl, cancer_genes_symbol, cn_bottom, cn_top)"},{"path":"https://umccr.github.io/rnasum/reference/purple_cnv_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get PURPLE CNV Summary — purple_cnv_summary","text":"tbl PURPLE gene CNV tibble cancer_genes_symbol Character vector gene symbols filter . cn_bottom CN threshold value classify genes within lost regions. cn_top CN threshold value classify genes within gained regions.","code":""},{"path":"https://umccr.github.io/rnasum/reference/purple_cnv_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PURPLE CNV Summary — purple_cnv_summary","text":"List genes, top bottom copy number thresholds.","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_cyto_info38.html","id":null,"dir":"Reference","previous_headings":"","what":"RCircos HG38 CytoBandIdeogram Object — rcircos_cyto_info38","title":"RCircos HG38 CytoBandIdeogram Object — rcircos_cyto_info38","text":"RCircos HG38 CytoBandIdeogram Object","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_cyto_info38.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RCircos HG38 CytoBandIdeogram Object — rcircos_cyto_info38","text":"","code":"rcircos_cyto_info38()"},{"path":"https://umccr.github.io/rnasum/reference/rcircos_cyto_info38.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"RCircos HG38 CytoBandIdeogram Object — rcircos_cyto_info38","text":"dataframe hg38 cytoband/ideogram information RCircos.","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"RCircos Plot — rcircos_plot","title":"RCircos Plot — rcircos_plot","text":"RCircos Plot","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RCircos Plot — rcircos_plot","text":"","code":"rcircos_plot(df_circos, df_circos_pairs, cyto.info)"},{"path":"https://umccr.github.io/rnasum/reference/rcircos_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RCircos Plot — rcircos_plot","text":"df_circos Dataframe 4 columns: Chromosome, chromStart, chromEnd, Gene. df_circos_pairs Dataframe 3 columns fusion mate: Chromosome, chromStart chromEnd geneA geneB. cyto.info dataframe hg38 cytoband/ideogram information RCircos.","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"RCircos Plot — rcircos_plot","text":"RCircos plot object.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Sample Data — read_sample_data","title":"Read Sample Data — read_sample_data","text":"Reads sample data, including Arriba fusions, Arriba plots, Salmon counts, DRAGEN fusions.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Sample Data — read_sample_data","text":"","code":"read_sample_data(p, results_dir, tx2gene = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Sample Data — read_sample_data","text":"p RNAsum params list. results_dir Directory output extracted Arriba PNGs (created automatically already exist). tx2gene data.frame tx_name gene_id columns. Required salmon. See tximport::tximport.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Sample Data — read_sample_data","text":"list input sample data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Sample Data — read_sample_data","text":"","code":"p <- list(   dragen_rnaseq = system.file(\"rawdata/test_data/dragen\", package = \"RNAsum\"),   arriba_pdf = system.file(\"rawdata/test_data/dragen/arriba/fusions.pdf\", package = \"RNAsum\"),   arriba_tsv = system.file(\"rawdata/test_data/dragen/arriba/fusions.tsv\", package = \"RNAsum\"),   dragen_fusions = system.file(     \"rawdata/test_data/dragen/test_sample_WTS.fusion_candidates.final\",     package = \"RNAsum\"   ),   umccrise = system.file(     \"rawdata/test_data/umccrised/test_sample_WGS\",     package = \"RNAsum\"   ),   manta_tsv = system.file(     \"rawdata/test_data/umccrised/test_sample_WGS/structural/manta.tsv\",     package = \"RNAsum\"   ) ) res <- read_sample_data(p, tempdir())"},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Read WGS Data — read_wgs_data","title":"Read WGS Data — read_wgs_data","text":"Reads WGS data, including PCGR tiers.tsv, PURPLE cnv.gene.tsv, Manta manta.tsv. file path specified RNAsum params valid, returned. fallback, umccrise directory param specified, attempt detect file pattern .","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read WGS Data — read_wgs_data","text":"","code":"read_wgs_data(p)"},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read WGS Data — read_wgs_data","text":"p RNAsum params list.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read WGS Data — read_wgs_data","text":"list input sample data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read WGS Data — read_wgs_data","text":"","code":"p <- list(   umccrise = system.file(\"rawdata/test_data/umccrised/test_sample_WGS\", package = \"RNAsum\"),   pcgr_tiers_tsv = system.file(     \"rawdata/test_data/umccrised/test_sample_WGS/small_variants\",     \"TEST-somatic.pcgr.snvs_indels.tiers.tsv\",     package = \"RNAsum\"   ),   manta_tsv = system.file(     \"rawdata/test_data/umccrised/test_sample_WGS/structural/TEST-prioritize-manta.tsv\",     package = \"RNAsum\"   ) ) (res <- read_wgs_data(p)) #> $pcgr_tiers_tsv #> # A tibble: 99 × 61 #>    CHROM POS       REF   ALT   GENOMIC_CHANGE    GENOME_VERSION VCF_SAMPLE_ID    #>    <chr> <chr>     <chr> <chr> <chr>             <chr>          <chr>            #>  1 3     179218303 G     A     3:g.179218303G>A  grch38         SBJ02999__PRJ22… #>  2 17    7674894   G     A     17:g.7674894G>A   grch38         SBJ02999__PRJ22… #>  3 13    110715614 C     G     13:g.110715614C>G grch38         SBJ02999__PRJ22… #>  4 13    110719444 G     C     13:g.110719444G>C grch38         SBJ02999__PRJ22… #>  5 8     20250093  C     T     8:g.20250093C>T   grch38         SBJ02999__PRJ22… #>  6 8     13086457  C     T     8:g.13086457C>T   grch38         SBJ02999__PRJ22… #>  7 10    31521795  G     C     10:g.31521795G>C  grch38         SBJ02999__PRJ22… #>  8 9     132927250 G     A     9:g.132927250G>A  grch38         SBJ02999__PRJ22… #>  9 3     47121452  G     A     3:g.47121452G>A   grch38         SBJ02999__PRJ22… #> 10 6     117365075 G     C     6:g.117365075G>C  grch38         SBJ02999__PRJ22… #> # ℹ 89 more rows #> # ℹ 54 more variables: VARIANT_CLASS <chr>, SYMBOL <chr>, GENE_NAME <chr>, #> #   CCDS <chr>, CANONICAL <chr>, ENTREZ_ID <chr>, UNIPROT_ID <chr>, #> #   ENSEMBL_TRANSCRIPT_ID <chr>, ENSEMBL_GENE_ID <chr>, REFSEQ_MRNA <chr>, #> #   ONCOSCORE <chr>, ONCOGENE <chr>, TUMOR_SUPPRESSOR <chr>, #> #   ONCOGENE_EVIDENCE <chr>, TUMOR_SUPPRESSOR_EVIDENCE <chr>, #> #   DISGENET_CUI <chr>, DISGENET_TERMS <chr>, CONSEQUENCE <chr>, … #>  #> $purple_gene_tsv #> # A tibble: 25,417 × 20 #>    chromosome  start    end gene        minCopyNumber maxCopyNumber unused #>    <chr>       <int>  <int> <chr>               <dbl>         <dbl> <chr>  #>  1 chr1        11869  14409 DDX11L1              1.98          1.98 0      #>  2 chr1        14404  29570 WASH7P               1.98          1.98 0      #>  3 chr1        17369  17436 MIR6859-1            1.98          1.98 0      #>  4 chr1        29554  31097 MIR1302-2HG          1.98          1.98 0      #>  5 chr1        30366  30503 MIR1302-2            1.98          1.98 0      #>  6 chr1        34554  36081 FAM138A              1.98          1.98 0      #>  7 chr1        69091  70008 OR4F5                1.98          1.98 0      #>  8 chr1       185217 195411 FO538757.1           1.98          1.98 0      #>  9 chr1       187891 187958 MIR6859-2            1.98          1.98 0      #> 10 chr1       450740 451678 OR4F29               1.98          1.98 0      #> # ℹ 25,407 more rows #> # ℹ 13 more variables: somaticRegions <dbl>, germlineHomDeletionRegions <dbl>, #> #   germlineHetToHomDeletionRegions <dbl>, transcriptId <chr>, #> #   transcriptVersion <chr>, chromosomeBand <chr>, minRegions <dbl>, #> #   minRegionStart <int>, minRegionEnd <int>, minRegionStartSupport <chr>, #> #   minRegionEndSupport <chr>, minRegionMethod <chr>, #> #   minMinorAlleleCopyNumber <dbl> #>  #> $manta_tsv #> $manta_tsv$unmelted #> # A tibble: 99 × 19 #>    vcfnum  nann TierTop Start         End    Type  BND_ID BND_mate SR_alt PR_alt #>    <chr>  <dbl> <chr>   <chr>         <chr>  <chr> <chr>  <chr>     <int>  <int> #>  1 68         1 4       1:107,176,815 orpha… BND   1      B             7      9 #>  2 69         1 4       1:107,177,428 orpha… BND   2      A            23     26 #>  3 76         1 4       1:114,885,352 orpha… BND   3      A            27     35 #>  4 01         1 4       1:2,652,000   1:NA   PURP… NA     NA           NA     NA #>  5 02         1 4       1:3,614,001   1:NA   PURP… NA     NA           NA     NA #>  6 03         1 4       1:6,593,001   1:NA   PURP… NA     NA           NA     NA #>  7 04         1 4       1:6,908,000   1:NA   PURP… NA     NA           NA     NA #>  8 05         1 4       1:7,714,001   1:NA   PURP… NA     NA           NA     NA #>  9 06         1 4       1:10,615,000  1:NA   PURP… NA     NA           NA     NA #> 10 07         1 4       1:12,123,001  1:NA   PURP… NA     NA           NA     NA #> # ℹ 89 more rows #> # ℹ 9 more variables: SR_PR_sum <int>, SR_PR_ref <chr>, Ploidy <dbl>, #> #   AF_PURPLE <chr>, AF_BPI <chr>, CNC <chr>, CN <chr>, SScore <int>, #> #   annotation <chr> #>  #> $manta_tsv$melted #> # A tibble: 186 × 28 #>    vcfnum  nann TierTop Start         End    Type  BND_ID BND_mate SR_alt PR_alt #>    <chr>  <dbl> <chr>   <chr>         <chr>  <chr> <chr>  <chr>     <int>  <int> #>  1 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  2 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  3 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  4 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  5 62         5 3       1:97,924,845  1:97,… DUP   NA     NA           21     15 #>  6 13         4 3       1:20,551,467  1:20,… DEL   NA     NA           11     21 #>  7 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  8 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  9 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #> 10 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #> # ℹ 176 more rows #> # ℹ 18 more variables: SR_PR_sum <int>, SR_PR_ref <chr>, Ploidy <dbl>, #> #   AF_PURPLE <chr>, AF_BPI <chr>, CNC <chr>, CN <chr>, SScore <int>, #> #   Event <chr>, Effect <chr>, Genes <chr>, Transcript <chr>, Detail <chr>, #> #   Tier <chr>, ntrx <dbl>, ngen <dbl>, neff <dbl>, `Tier (Top)` <glue> #>  #> $manta_tsv$tsv_descr #> # A tibble: 23 × 3 #>    Column             Description                                          Type  #>    <chr>              <chr>                                                <chr> #>  1 caller             Manta SV caller                                      c     #>  2 sample             Tumor sample name                                    c     #>  3 chrom              CHROM column in VCF                                  c     #>  4 start              POS column in VCF                                    i     #>  5 end                INFO/END: End position of the variant described in … i     #>  6 svtype             INFO/SVTYPE: Type of structural variant              c     #>  7 split_read_support FORMAT/SR of tumor sample: Split reads for the ref … c     #>  8 paired_support_PE  FORMAT/PE of tumor sample: ??                        c     #>  9 paired_support_PR  FORMAT/PR of tumor sample: Spanning paired-read sup… c     #> 10 AF_BPI             INFO/BPI_AF: AF at each breakpoint (so AF_BPI1,AF_B… c     #> # ℹ 13 more rows #>  #> $manta_tsv$col_descr #> # A tibble: 30 × 2 #>    Column     Description                                                        #>    <chr>      <chr>                                                              #>  1 nrow       \"Row number that connects variants between tables in same tab set… #>  2 vcfnum     \"Original event row number that connects variants to events.\"      #>  3 TierTop    \"Top priority of the event (from simple_sv_annotation: 1 highest,… #>  4 Tier       \"Priority of the specific event (from simple_sv_annotation: 1 hig… #>  5 Tier (Top) \"Priority of the specific event (Top tier of all event's annotati… #>  6 Chr        \"Chromosome.\"                                                      #>  7 Start      \"Start position as inferred by BPI. For PURPLE-inferred SVs we us… #>  8 End        \"End position. For BNDs = Chr:Start of the mate.Values are inferr… #>  9 ID         \"ID of BND from Manta. For PURPLE-inferred SVs this is PURPLE.\"    #> 10 MATEID     \"ID of BND mate from Manta.\"                                       #> # ℹ 20 more rows #>  #>"},{"path":"https://umccr.github.io/rnasum/reference/rnasum_rmd.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate UMCCR RNAsum Report — rnasum_rmd","title":"Generate UMCCR RNAsum Report — rnasum_rmd","text":"Generates UMCCR RNAsum HTML report. following steps: copy rmd tmp/rnasum.Rmd render rmd inside tmp/ return path output HTML","code":""},{"path":"https://umccr.github.io/rnasum/reference/rnasum_rmd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate UMCCR RNAsum Report — rnasum_rmd","text":"","code":"rnasum_rmd(out_file = NULL, quiet = FALSE, pars)"},{"path":"https://umccr.github.io/rnasum/reference/rnasum_rmd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate UMCCR RNAsum Report — rnasum_rmd","text":"out_file Path output HTML file (needs '.html' suffix). quiet Suppress printing rendering. pars List named parameters override custom params specified within Rmd's YAML front-matter.","code":""},{"path":"https://umccr.github.io/rnasum/reference/rnasum_rmd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate UMCCR RNAsum Report — rnasum_rmd","text":"Path rendered HTML report.","code":""},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Salmon Counts — salmon_counts","title":"Get Salmon Counts — salmon_counts","text":"Get salmon counts via tximport.","code":""},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Salmon Counts — salmon_counts","text":"","code":"salmon_counts(x, tx2gene = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Salmon Counts — salmon_counts","text":"x Path quant.sf file abundances. See tximport::tximport. tx2gene data.frame tx_name gene_id columns. See tximport::tximport.","code":""},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Salmon Counts — salmon_counts","text":"Tibble counts per gene transcript, NULL input params NULL.","code":""},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Salmon Counts — salmon_counts","text":"","code":"x <- system.file(\"rawdata/test_data/dragen/TEST.quant.sf\", package = \"RNAsum\") tx2gene <- NULL (sc <- salmon_counts(x, tx2gene)) # NULL since no tx2gene specified #> NULL"},{"path":"https://umccr.github.io/rnasum/reference/saveWidgetFix.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for saveWidget bug fix — saveWidgetFix","title":"Wrapper for saveWidget bug fix — saveWidgetFix","text":"wrapper saveWidget compensates bug temporary directory widget dependencies deleted - see https://github.com/ramnathv/htmlwidgets/issues/296.","code":""},{"path":"https://umccr.github.io/rnasum/reference/saveWidgetFix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for saveWidget bug fix — saveWidgetFix","text":"","code":"saveWidgetFix(widget, file, selfcontained = TRUE, ...)"},{"path":"https://umccr.github.io/rnasum/reference/saveWidgetFix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for saveWidget bug fix — saveWidgetFix","text":"widget Widget save. file Full path save HTML . selfcontained Whether save HTML single self-contained file (external resources base64 encoded) file external resources placed adjacent directory. ... Additional arguments passed htmlwidgets::saveWidget.","code":""},{"path":"https://umccr.github.io/rnasum/reference/saveWidgetFix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for saveWidget bug fix — saveWidgetFix","text":"Change work dir compensate saveWidget bug","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_kable.html","id":null,"dir":"Reference","previous_headings":"","what":"Session Information Kable — session_info_kable","title":"Session Information Kable — session_info_kable","text":"Session information kables vignettes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_kable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Session Information Kable — session_info_kable","text":"","code":"session_info_kable(pkgs = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/session_info_kable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Session Information Kable — session_info_kable","text":"pkgs Vector R packages display vignette. default returns .","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_kable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Session Information Kable — session_info_kable","text":"list two kables containing information platform specified packages.","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_tbls.html","id":null,"dir":"Reference","previous_headings":"","what":"Session Information Tables — session_info_tbls","title":"Session Information Tables — session_info_tbls","text":"Session information tables.","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_tbls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Session Information Tables — session_info_tbls","text":"","code":"session_info_tbls(pkgs = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/session_info_tbls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Session Information Tables — session_info_tbls","text":"pkgs Vector R packages display vignette. default returns .","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_tbls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Session Information Tables — session_info_tbls","text":"list two tibbles containing information platform specified packages.","code":""},{"path":"https://umccr.github.io/rnasum/reference/sv_manta_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Manta SV Summary — sv_manta_summary","title":"Get Manta SV Summary — sv_manta_summary","text":"Get Manta SV Summary","code":""},{"path":"https://umccr.github.io/rnasum/reference/sv_manta_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Manta SV Summary — sv_manta_summary","text":"","code":"sv_manta_summary(tbl)"},{"path":"https://umccr.github.io/rnasum/reference/sv_manta_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Manta SV Summary — sv_manta_summary","text":"tbl Tibble melted SVs umccrise, containing 'Genes' column.","code":""},{"path":"https://umccr.github.io/rnasum/reference/sv_manta_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Manta SV Summary — sv_manta_summary","text":"Character vector Genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://www.tidyverse.org/blog/2019/06/rlang-0-4-0/","code":""},{"path":"https://umccr.github.io/rnasum/reference/tpm_from_rpkm.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate TPM from RPKM — tpm_from_rpkm","title":"Calculate TPM from RPKM — tpm_from_rpkm","text":"Calculate TPM RPKM (http://luisvalesilva.com/datasimple/rna-seq_units.html )","code":""},{"path":"https://umccr.github.io/rnasum/reference/tpm_from_rpkm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate TPM from RPKM — tpm_from_rpkm","text":"","code":"tpm_from_rpkm(x)"},{"path":"https://umccr.github.io/rnasum/reference/tpm_from_rpkm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate TPM from RPKM — tpm_from_rpkm","text":"x RPKM values","code":""},{"path":"https://umccr.github.io/rnasum/reference/tpm_from_rpkm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate TPM from RPKM — tpm_from_rpkm","text":"TPM values","code":""},{"path":"https://umccr.github.io/rnasum/reference/webplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate spider web plots to present immunogram genes — webplot","title":"Generate spider web plots to present immunogram genes — webplot","text":"Generate spider web plots present immunogram genes (http://www.statisticstoproveanything.com/2013/11/spider-web-plots--r.html).","code":""},{"path":"https://umccr.github.io/rnasum/reference/webplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate spider web plots to present immunogram genes — webplot","text":"","code":"webplot(   data,   data.row = NULL,   y.cols = NULL,   main = NULL,   add = F,   col = \"red\",   lty = 1,   scale = T )"},{"path":"https://umccr.github.io/rnasum/reference/webplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate spider web plots to present immunogram genes — webplot","text":"data Dataframe matrix. data.row Row data plot (NULL uses row 1). y.cols Columns interest (NULL selects numeric columns). main Title plot (NULL rowname data). add Whether plot added existing plot. col Color data line lty Lty data line scale Scale.","code":""},{"path":"https://umccr.github.io/rnasum/reference/webplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate spider web plots to present immunogram genes — webplot","text":"Spider web plots present immunogram genes","code":""}]
+[{"path":"https://umccr.github.io/rnasum/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 RNAsum authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://umccr.github.io/rnasum/articles/development.html","id":"ref_dataset-list","dir":"Articles","previous_headings":"","what":"ref_dataset.list","title":"Development","text":"Processed data following elements:","code":""},{"path":"https://umccr.github.io/rnasum/articles/development.html","id":"ref_genes-list","dir":"Articles","previous_headings":"","what":"ref_genes.list","title":"Development","text":"Genes interest following gene sets:","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"input-data","dir":"Articles","previous_headings":"","what":"Input data","title":"RNAsum Sections","text":"Summary input data","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"clinical-information","dir":"Articles","previous_headings":"","what":"Clinical information","title":"RNAsum Sections","text":"Treatment regimen information patient clinical information available. NOTE: confidentiality reasons, timeline (x-axis) projecting patient’s treatment regimens (y-axis) set start 1st January 2000, treatments lengths preserved.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"findings-summary","dir":"Articles","previous_headings":"","what":"Findings summary","title":"RNAsum Sections","text":"Plot table summarising altered genes listed across various report sections","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"mutated-genes","dir":"Articles","previous_headings":"","what":"Mutated genes","title":"RNAsum Sections","text":"mRNA expression levels mutated genes (containing single nucleotide variants (SNVs) insertions/deletions (indels)) measured patient’s sample average mRNA expression samples cancer patients (TCGA). section available samples available umccrise results.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"fusion-genes","dir":"Articles","previous_headings":"","what":"Fusion genes","title":"RNAsum Sections","text":"Prioritised fusion genes based arriba results annotated FusionGDB database. WGS results umccrise available fusion genes Fusion genes report section ordered based evidence genome-based data. information gene fusions methods detection visualisation can found fusions dir.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"prioritisation","dir":"Articles","previous_headings":"Fusion genes","what":"Prioritisation","title":"RNAsum Sections","text":"Fusion genes detected transcriptome data prioritised based criteria ranked following order: Involvement fusion gene(s) detected genomic data (Structural variants results available) Detected transcriptome data arriba Reported fusion event according FusionGDB database Decreasing number split reads Decreasing number pair reads Involvement cancer gene(s) (see Cancer genes section)","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"filtering","dir":"Articles","previous_headings":"Fusion genes","what":"Filtering","title":"RNAsum Sections","text":"Fusion genes detected transcriptome data reported least one following criteria met: Involvement fusion gene(s) detected genomic data (SV results available) Reported fusion event according FusionGDB database Involvement cancer gene(s) (see Cancer genes section) Split reads > 1 Pair reads > 1 split reads > 1","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"structural-variants","dir":"Articles","previous_headings":"","what":"Structural variants","title":"RNAsum Sections","text":"Similar Mutated genes analysis limited genes located within SVs detected Manta using genomic data. section available samples available Manta results.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"cn-altered-genes","dir":"Articles","previous_headings":"","what":"CN altered genes","title":"RNAsum Sections","text":"Section overlaying mRNA expression data cancer genes per-gene somatic copy-number (CN) data (PURPLE) mutation status, available.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"immune-markers","dir":"Articles","previous_headings":"","what":"Immune markers","title":"RNAsum Sections","text":"Similar Mutated genes analysis limited genes considered immune markers. immune markers used report listed PanelApp panel Immune markers WTS report.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"hrd-genes","dir":"Articles","previous_headings":"","what":"HRD genes","title":"RNAsum Sections","text":"Similar Mutated genes analysis limited genes considered homologous recombination deficiency (HRD) genes. HRD genes used report listed PanelApp panel Homologous recombination deficiency (HDR) WTS report.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"cancer-genes","dir":"Articles","previous_headings":"","what":"Cancer genes","title":"RNAsum Sections","text":"Similar analysis , limited UMCCR cancer genes.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"drug-matching","dir":"Articles","previous_headings":"","what":"Drug matching","title":"RNAsum Sections","text":"List drugs targeting variants detected mutated genes, fusion genes, structural variants-affected genes, CN altered genes, HRD genes dysregulated cancer genes, can considered treatment decision making process. Note section displayed default. Set --drugs argument TRUE present report.","code":""},{"path":"https://umccr.github.io/rnasum/articles/report_structure.html","id":"addendum","dir":"Articles","previous_headings":"","what":"Addendum","title":"RNAsum Sections","text":"Additional information, including Parameters, Reporter details R Session information, added end report.","code":""},{"path":"https://umccr.github.io/rnasum/articles/tcga_projects_summary.html","id":"primary-datasets","dir":"Articles","previous_headings":"","what":"Primary datasets","title":"TCGA Projects","text":"table summarises TCGA expression data available 33 cancer types. NOTE: reduce data processing time size final RNAsum HTML report, following datasets restricted include expression data 300 patients: BRCA, THCA, HNSC, LGG, KIRC, LUSC, LUAD, PRAD, STAD LIHC.","code":""},{"path":"https://umccr.github.io/rnasum/articles/tcga_projects_summary.html","id":"extended-datasets","dir":"Articles","previous_headings":"","what":"Extended datasets","title":"TCGA Projects","text":"extended sets available BLCA, PAAD, LUAD cohorts, including neuroendocrine tumours (NETs), intraductal papillary mucinous neoplasm (IPMNs), acinar cell carcinoma (ACC) samples large-cell neuroendocrine carcinoma (LCNEC).","code":""},{"path":"https://umccr.github.io/rnasum/articles/tcga_projects_summary.html","id":"pan-cancer-dataset","dir":"Articles","previous_headings":"","what":"Pan-Cancer dataset","title":"TCGA Projects","text":"10 samples 33 datasets combined create Pan-Cancer dataset. * Tissue codes: ** dataset cleaned based quality metrics provided Merged Sample Quality Annotations file (TSV available ), linked TCGA PanCanAtlas initiative webpage (see TCGA-data-harmonization repository details, including sample inclusion criteria).","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"data-collection","dir":"Articles","previous_headings":"","what":"1. Data collection","title":"Workflow Details","text":"Read counts data patient collected DRAGEN RNA bcbio-nextgen RNA-seq pipeline.","code":""},{"path":[]},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"counts-processing","dir":"Articles","previous_headings":"2. Data processing","what":"Counts processing","title":"Workflow Details","text":"read count data (e.g. abundance.tsv quant.sf quantification files kallisto salmon, respectively) processed according steps illustrated described . Figure 1 Counts processing scheme.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"data-collection---fig1a","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Data collection - Fig1A","title":"Workflow Details","text":"patient sample external reference cohort UMCCR internal reference set -house pancreatic cancer samples","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"transformation---fig1b","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Transformation - Fig1B","title":"Workflow Details","text":"Subset datasets include common genes Combine patient sample internal reference dataset sample + internal reference set external reference set","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"filtering-optional---fig1c","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Filtering (optional) - Fig1C","title":"Workflow Details","text":"sample + internal reference set external reference set","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"normalisation-optional---fig1d","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Normalisation (optional) - Fig1D","title":"Workflow Details","text":"sample + internal reference set external reference set","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"combination---fig1e","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Combination - Fig1E","title":"Workflow Details","text":"Subset datasets include common genes Combine sample + internal reference set external reference set","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"batch-effects-correction-optional---fig1f","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Batch-effects correction (optional) - Fig1F","title":"Workflow Details","text":"Consider patient sample + internal reference (regardless patient sample origin) one batch (sets processed pipeline) corresponding TCGA dataset another batch. objective remove data variation due technical factors.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"data-scaling","dir":"Articles","previous_headings":"2. Data processing > Counts processing","what":"Data scaling","title":"Workflow Details","text":"processed count data scaled facilitate interpretation expression values. data either scaled: - gene-wise (Z-score transformation, default) - group-wise (centering).","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"gene-wise","dir":"Articles","previous_headings":"2. Data processing > Counts processing > Data scaling","what":"Gene-wise","title":"Workflow Details","text":"Z-scores comparable measuring observations multiples standard deviation given sample. gene-wise Z-score transformation procedure illustrated described . Figure 2 Gene-wise Z-score transformation scheme.  Extract expression values across samples given gene (Fig2A) Compute Z-scores individual samples (see equation Fig2B) internal reference set* external reference set Present patient sample Z-score context reference cohorts’ median Z-scores (Fig2D). * used pancreatic cancer patients","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"group-wise","dir":"Articles","previous_headings":"2. Data processing > Counts processing > Data scaling","what":"Group-wise","title":"Workflow Details","text":"group-wise centering apporach illustrated described . Figure 3 Group-wise centering scheme.  patient sample internal reference set* external reference set internal reference set* external reference set Center median expression values gene individual groups (Fig3C). Present patient sample centered expression values context reference cohorts’ centered values (Fig3D). * used pancreatic cancer patients","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"integration-with-wgs-based-results","dir":"Articles","previous_headings":"","what":"3. Integration with WGS-based results","title":"Workflow Details","text":"patients available WGS data processed using umccrise pipeline, expression level information mutated genes genes located within detected SVs/CNVs, well genome-based findings, incorporated used primary source expression profile prioritisation.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"somatic-snvs-and-small-indels","dir":"Articles","previous_headings":"3. Integration with WGS-based results","what":"Somatic SNVs and small indels","title":"Workflow Details","text":"Check PCGR tiered TSV output file available (e.g. ). Extract expression level information genome-based findings genes detected genomic variants (use --pcgr_tier argument define tier threshold value). Order genes increasing variant tier decreasing absolute values representing difference expression levels patient sample corresponding reference cohort.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"structural-variants","dir":"Articles","previous_headings":"3. Integration with WGS-based results","what":"Structural variants","title":"Workflow Details","text":"Check Manta annotated TSV output file available (e.g. example input). Extract expression level information genome-based findings genes located within detected SVs Order genes increasing SV score decreasing absolute values representing difference expression levels patient sample corresponding reference cohort. Compare gene fusions detected WTS data (arriba pizzly) WGS data (Manta) Prioritise WGS-supported gene fusions.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"somatic-cnvs","dir":"Articles","previous_headings":"3. Integration with WGS-based results","what":"Somatic CNVs","title":"Workflow Details","text":"Check PURPLE output file available (e.g. example input). Extract expression level information genome-based findings genes located within detected CNVs (use --cn_loss --cn_gain arguments define CN threshold values classify genes within lost gained regions). Order genes increasing (genes within lost regions) decreasing (genes within gained regions) Copy Number decreasing absolute values representing difference expression levels patient sample corresponding reference cohort.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"results-annotation","dir":"Articles","previous_headings":"","what":"4. Results annotation","title":"Workflow Details","text":"WTS- /WGS-based results altered genes collated knowledge derived -house resources public databases (listed ), provide additional sources evidence significance, e.g. flag variants clinical significance potential druggable targets.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"key-cancer-genes","dir":"Articles","previous_headings":"4. Results annotation","what":"Key cancer genes","title":"Workflow Details","text":"UMCCR cancer gene panel builds several sources: Cancermine least 2 publications least 3 citations NCG known cancer genes Tier 1 COSMIC Cancer Gene Census (CGC) CACAO hotspot genes (curated ClinVar, CiViC, Cancer Hotspots) Cancer predisposition genes (CPSR list) COSMIC Cancer Gene Census (tier 2) AstraZeneca 300 (AZ300) Familial Cancer OncoKB annotated MSKC-IMPACT MSKC-Heme PMCC-CCP Illumina-TS500 TEMPUS Foundation One Foundation Heme Vogelstein Used extracting expression levels cancer genes (presented Cancer genes report section) Used prioritise candidate fusion genes","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"oncokb","dir":"Articles","previous_headings":"4. Results annotation","what":"OncoKB","title":"Workflow Details","text":"OncoKB gene list used annotate altered genes across various sections report (annotations URL links External resources column report Summary tables).","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"vicc","dir":"Articles","previous_headings":"4. Results annotation","what":"VICC","title":"Workflow Details","text":"Variant Interpretation Cancer Consortium (VICC) knowledgebase used annotate altered genes across various sections report (annotations URL links External resources column report Summary tables).","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"civic","dir":"Articles","previous_headings":"4. Results annotation","what":"CIViC","title":"Workflow Details","text":"Clinical Interpretation Variants Cancer (CIViC) database used annotate altered genes across various sections report (annotations URL links External resources column report Summary tables). Used flag clinically actionable aberrations Drug matching report section.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"cgi","dir":"Articles","previous_headings":"4. Results annotation","what":"CGI","title":"Workflow Details","text":"Cancer Genome Interpreter (CGI) database used flag genes known involved gene fusions prioritise candidate fusion genes.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"fusiongdb","dir":"Articles","previous_headings":"4. Results annotation","what":"FusionGDB","title":"Workflow Details","text":"FusionGDB database used flag genes known involved gene fusions prioritise candidate gene fusions.","code":""},{"path":"https://umccr.github.io/rnasum/articles/workflow.html","id":"report-generation","dir":"Articles","previous_headings":"4. Results annotation","what":"5. Report generation","title":"Workflow Details","text":"final RNAsum HTML Patient Transcriptome Summary report contains searchable tables interactive plots presenting expression levels altered genes, well links public resources providing additional source evidence significance.","code":""},{"path":"https://umccr.github.io/rnasum/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sehrish Kanwal. Author, maintainer. Jacek Marzec. Author.","code":""},{"path":"https://umccr.github.io/rnasum/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kanwal S, Marzec J (2023). RNAsum: Robust Tool Performing Transcriptome Profiling Cancer Data. https://umccr.github.io/RNAsum/, https://github.com/umccr/RNAsum.","code":"@Manual{,   title = {RNAsum: A Robust Tool for Performing Transcriptome Profiling on Cancer Data},   author = {Sehrish Kanwal and Jacek Marzec},   year = {2023},   note = {https://umccr.github.io/RNAsum/, https://github.com/umccr/RNAsum}, }"},{"path":"https://umccr.github.io/rnasum/index.html","id":"rnasum","dir":"","previous_headings":"","what":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"RNAsum R package can post-process, summarise visualise outputs primarily DRAGEN RNA pipelines. main application complement genome-based findings umccrise pipeline provide additional evidence detected alterations. DOCS: https://umccr.github.io/RNAsum","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"R package can installed directly GitHub source: Conda package available Anaconda umccr channel: Docker image available GitHub Container Registy:","code":"remotes::install_github(\"umccr/RNAsum\") # latest master commit remotes::install_github(\"umccr/RNAsum@v0.0.X\") # version 0.0.X remotes::install_github(\"umccr/RNAsum@abcde\") # commit abcde remotes::install_github(\"umccr/RNAsum#123\") # PR 123 conda install r-rnasum==0.0.X -c umccr -c conda-forge -c bioconda docker pull ghcr.io/umccr/rnasum:latest"},{"path":"https://umccr.github.io/rnasum/index.html","id":"workflow","dir":"","previous_headings":"","what":"Workflow","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"pipeline consists five main components illustrated briefly described . details, see workflow.md.  Collect patient WTS data DRAGEN RNA pipeline including per-gene read counts gene fusions. Add expression data reference cohorts get idea expression levels genes interest cancer patient cohorts. read counts normalised, transformed converted scale allows present patient’s expression measurements context reference cohorts. Supply genome-based findings whole-genome sequencing (WGS) data focus genes interest provide additional evidence dysregulation mutated genes, genes located within detected structural variants (SVs) copy-number (CN) altered regions. RNAsum designed compatible WGS patient outputs generated umccrise. Collate results knowledge derived -house resources public databases provide additional sources evidence clinical significance altered genes e.g. flag variants clinical significance potential druggable targets. final product interactive HTML report searchable tables plots presenting expression levels genes interest. report consists several sections described .","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"reference-data","dir":"","previous_headings":"","what":"Reference data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"reference expression data available 33 cancer types derived external (TCGA) internal (UMCCR) resources.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"external-reference-cohorts","dir":"","previous_headings":"Reference data","what":"External reference cohorts","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"order explore expression changes patient, built high-quality pancreatic cancer reference cohort. Depending tissue patient’s sample taken, one 33 cancer datasets TCGA can used reference cohort comparing expression changes genes interest patient. Additionally, 10 samples 33 TCGA datasets combined create Pan-Cancer dataset, cohorts extended sets also available. available datasets listed TCGA projects summary table. datasets processed using methods described TCGA-data-harmonization repository. dataset interest can specified using one TCGA project IDs RNAsum --dataset argument (see Examples).","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"internal-reference-cohort","dir":"","previous_headings":"Reference data","what":"Internal reference cohort","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"publicly available TCGA datasets expected demonstrate prominent batch effects compared -house WTS data due differences applied experimental procedures analytical pipelines. Moreover, TCGA data may include samples tissue material lower quality cellularity compared samples processed using local protocols. address issues, built high-quality internal reference cohort processed using pipelines input data (see data pre-processing). internal reference set 40 pancreatic cancer samples based WTS data generated UMCCR processed bcbio-nextgen RNA-seq pipeline minimise potential batch effects investigated samples reference cohort make sure data comparable. internal reference cohort assembly summarised Pancreatic-data-harmonization repository. Note two rationales using internal reference cohort: batch effects correction reference point comparing per-gene expression levels observed data patient interest data pancreatic cancer patients. case samples cancer type data internal reference cohort used batch effects correction procedure performed minimise technical-related variation data.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"input-data","dir":"","previous_headings":"","what":"Input data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"RNAsum accepts WTS data processed DRAGEN RNA pipeline. Additionally, WTS data can integrated WGS-based data processed using umccrise pipeline. latter case, genome-based findings corresponding patient sample incorporated report used primary source expression profile prioritisation.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"wts","dir":"","previous_headings":"Input data","what":"WTS","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"required WTS input data read counts provided quantification file DRAGEN RNA pipeline.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"dragen-rna","dir":"","previous_headings":"Input data > WTS","what":"DRAGEN RNA","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"table lists input data accepted RNAsum: files expected organised following structure:","code":"| |____<SampleName>   |____<SampleName>quant.sf   |____<SampleName>.fusion_candidates.final"},{"path":"https://umccr.github.io/rnasum/index.html","id":"wgs","dir":"","previous_headings":"Input data","what":"WGS","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"RNAsum designed compatible WGS outputs generated umccrise. table lists input data accepted RNAsum: files expected organised following structure:","code":"| |____umccrised   |____<SampleName>     |____pcgr     | |____<SampleName>-somatic.pcgr.snvs_indels.tiers.tsv     |____purple     | |____<SampleName>.purple.gene.cnv     |____structural       |____<SampleName>-manta.tsv"},{"path":"https://umccr.github.io/rnasum/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"Note Human reference genome GRCh38 (Ensembl based annotation version 86) used gene annotation default. GRCh37 longer supported.","code":"rnasum_cli=$(Rscript -e 'x = system.file(\"cli\", package = \"RNAsum\"); cat(x, \"\\n\")' | xargs) export PATH=\"${rnasum_cli}:${PATH}\" $ rnasum.R --version rnasum.R x.x.x  $ rnasum.R --help Usage =====   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RNAsum/cli/rnasum.R [options]   Options ======= --arriba_pdf=ARRIBA_PDF         File path of Arriba PDF output  --arriba_tsv=ARRIBA_TSV         File path of Arriba TSV output  --batch_rm=BATCH_RM         Remove batch-associated effects between datasets? [def: TRUE]  --cn_gain=CN_GAIN         CN threshold value to classify genes within gained regions [def: 95]  --cn_loss=CN_LOSS         CN threshold value to classify genes within lost regions [def: 5]  --dataset=DATASET         Dataset to be used as external reference cohort [def: PANCAN]  --dataset_name_incl=DATASET_NAME_INCL         Include dataset in report name? [def: FALSE]  --dragen_fusions=DRAGEN_FUSIONS         File path to DRAGEN RNA-seq 'fusion_candidates.final' output  --drugs=DRUGS         Include drug matching section in report? [def: FALSE]  --filter=FILTER         Filter out low expressed genes? [def: TRUE]  --hide_code_btn=HIDE_CODE_BTN         Hide \"Code\" button above code chunks in report? [def: TRUE]  --immunogram=IMMUNOGRAM         Include immunogram in report? [def: FALSE]  --log=LOG         Log2 transform data before normalisation? [def: TRUE]  --manta_tsv=MANTA_TSV         File path to umccrise 'manta.tsv' output  --norm=NORM         Normalisation method  --pcgr_splice_vars=PCGR_SPLICE_VARS         Include non-coding splice region variants reported in PCGR? [def: TRUE]  --pcgr_tier=PCGR_TIER         Tier threshold for reporting variants reported in PCGR [def: 4]  --pcgr_tiers_tsv=PCGR_TIERS_TSV         File path to PCGR 'snvs_indels.tiers.tsv' output  --project=PROJECT         Project name  --purple_gene_tsv=PURPLE_GENE_TSV         File path to PURPLE 'purple.cnv.gene.tsv' output  --report_dir=REPORT_DIR         Directory path to output report  --salmon=SALMON         File path to salmon 'quant.sf' output  --sample_name=SAMPLE_NAME         Sample name to be presented in report  --sample_source=SAMPLE_SOURCE         Type of investigated sample [def: -]  --save_tables=SAVE_TABLES         Save interactive summary tables as HTML? [def: TRUE]  --scaling=SCALING         Scaling for z-score transformation (gene-wise or group-wise) [def: gene-wise]  --subject_id=SUBJECT_ID         Subject ID  --top_genes=TOP_GENES         Number of top ranked genes to be presented in report  --transform=TRANSFORM         Transformation method to be used when converting read counts [def: CPM]  --umccrise=UMCCRISE         Directory path of the corresponding WGS-related data  --help, -h         Show this help message and exit"},{"path":"https://umccr.github.io/rnasum/index.html","id":"examples","dir":"","previous_headings":"Usage","what":"Examples","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"RNAsum CLI commands generating HTML reports different data availability scenarios: WTS data WTS WGS data WTS WGS clinical data Note Example data provided /inst/rawdata/test_data folder GitHub repo. RNAsum runtime less 20 minutes using 16GB RAM memory 1 CPU.","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"id_1-wts-and-wgs-data","dir":"","previous_headings":"Usage > Examples","what":"1. WTS and WGS data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"frequent preferred case, WGS-based findings used primary source expression profile prioritisation. genome-based results can incorporated report specifying location corresponding umccrise output files (including results PCGR, PURPLE, Manta) using --umccrise argument. Mutated genes, Structural variants CN altered genes report sections contain information expression levels mutated genes, genes located within detected SVs CN altered regions, respectively. results Fusion genes section ordered based evidence genome-based data. subset TCGA pancreatic adenocarcinoma dataset used reference cohort (--dataset TEST). HTML report test_sample_WTS.RNAsum.html created inst/rawdata/test_data/dragen/RNAsum folder.","code":"rnasum.R \\   --sample_name test_sample_WTS \\   --dataset TEST \\   --dragen_rnaseq inst/rawdata/test_data/dragen \\   --report_dir inst/rawdata/test_data/dragen/RNAsum \\   --umccrise inst/rawdata/test_data/umccrised/test_sample_WGS \\   --save_tables FALSE"},{"path":"https://umccr.github.io/rnasum/index.html","id":"id_2-wts-data-only","dir":"","previous_headings":"Usage > Examples","what":"2. WTS data only","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"scenario, WTS data used expression levels key UMCCR Cancer genes, Fusion genes, Immune markers homologous recombination deficiency genes (HRD genes) reported. Moreover, gene fusions reported Fusion genes report section contain information evidence genome-based data. subset TCGA pancreatic adenocarcinoma dataset used reference cohort (--dataset TEST). output HTML report test_sample_WTS.RNAsum.html created inst/rawdata/test_data/dragen/RNAsum folder.","code":"rnasum.R \\   --sample_name test_sample_WTS \\   --dataset TEST \\   --dragen_rnaseq inst/rawdata/test_data/dragen \\   --report_dir inst/rawdata/test_data/dragen/RNAsum \\   --save_tables FALSE"},{"path":"https://umccr.github.io/rnasum/index.html","id":"id_3-wts-wgs-and-clinical-data","dir":"","previous_headings":"Usage > Examples","what":"3. WTS WGS and clinical data","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"samples derived subjects, clinical information available, treatment regimen timeline can added HTML report. can added specifying location relevant excel spreadsheet (see example test_clinical_data.xlsx inst/rawdata/test_data/test_clinical_data.xlsx) using --clinical_info argument. spreadsheet, least one following columns expected: NEOADJUVANT REGIMEN, ADJUVANT REGIMEN, FIRST LINE REGIMEN, SECOND LINE REGIMEN THIRD LINE REGIMEN, along START STOP dates corresponding treatments. subset TCGA pancreatic adenocarcinoma dataset used reference cohort (--dataset TEST). HTML report test_sample_WTS.RNAsum.html created ../rawdata/test_data/stratus/test_sample_WTS_dragen_v3.9.3/RNAsum folder.","code":"rnasum.R \\   --sample_name test_sample_WTS \\   --dataset TEST \\   --dragen_rnaseq $(pwd)/../rawdata/test_data/dragen \\   --report_dir $(pwd)/../rawdata/test_data/dragen/RNAsum \\   --umccrise $(pwd)/../rawdata/test_data/umccrised/test_sample_WGS \\   --save_tables FALSE \\   --clinical_info $(pwd)/../rawdata/test_data/test_clinical_data.xlsx \\   --save_tables FALSE"},{"path":"https://umccr.github.io/rnasum/index.html","id":"output","dir":"","previous_headings":"Usage","what":"Output","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"pipeline generates HTML Patient Transcriptome Summary report results folder:","code":"| |____<output>   |____<SampleName>.<output>.html   |____results     |____exprTables     |____glanceExprPlots     |____..."},{"path":"https://umccr.github.io/rnasum/index.html","id":"report","dir":"","previous_headings":"Usage > Output","what":"Report","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"generated HTML report includes searchable tables interactive plots presenting expression levels altered genes, well links public resources describing genes interest. report consists several sections, including: Input data Clinical information* Findings summary Mutated genes** Fusion genes Structural variants** CN altered genes** Immune markers HRD genes Cancer genes Drug matching * clinical information available; see --clinical_info argument  ** genome-based results available; see --umccrise argument Detailed description report structure, including result prioritisation visualisation available .","code":""},{"path":"https://umccr.github.io/rnasum/index.html","id":"results","dir":"","previous_headings":"Usage > Output","what":"Results","title":"A Robust Tool for Performing Transcriptome Profiling on Cancer Data","text":"results folder contains intermediate files, including plots tables presented HTML report.","code":""},{"path":"https://umccr.github.io/rnasum/reference/CapStr.html","id":null,"dir":"Reference","previous_headings":"","what":"Capitalise input string — CapStr","title":"Capitalise input string — CapStr","text":"Capitalises input string.","code":""},{"path":"https://umccr.github.io/rnasum/reference/CapStr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capitalise input string — CapStr","text":"","code":"CapStr(x)"},{"path":"https://umccr.github.io/rnasum/reference/CapStr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capitalise input string — CapStr","text":"x Input string.","code":""},{"path":"https://umccr.github.io/rnasum/reference/CapStr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capitalise input string — CapStr","text":"Capitalised string.","code":""},{"path":"https://umccr.github.io/rnasum/reference/REFERENCE_DATASETS.html","id":null,"dir":"Reference","previous_headings":"","what":"RNAsum Reference Datasets — REFERENCE_DATASETS","title":"RNAsum Reference Datasets — REFERENCE_DATASETS","text":"Reference datasets available RNAsum.","code":""},{"path":"https://umccr.github.io/rnasum/reference/REFERENCE_DATASETS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RNAsum Reference Datasets — REFERENCE_DATASETS","text":"","code":"data(REFERENCE_DATASETS)"},{"path":"https://umccr.github.io/rnasum/reference/REFERENCE_DATASETS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"RNAsum Reference Datasets — REFERENCE_DATASETS","text":"list lists project abbreviation code, name, tissue code number samples 40 datasets.","code":""},{"path":"https://umccr.github.io/rnasum/reference/RNAsum-package.html","id":null,"dir":"Reference","previous_headings":"","what":"RNAsum: A Robust Tool for Performing Transcriptome Profiling on Cancer Data — RNAsum-package","title":"RNAsum: A Robust Tool for Performing Transcriptome Profiling on Cancer Data — RNAsum-package","text":"RNA-seq reporting workflow designed post-process, summarise visualise output bcbio-nextgen RNA-seq Dragen RNA pipelines. main application complement genome-based findings provide additional evidence detected alterations.","code":""},{"path":[]},{"path":"https://umccr.github.io/rnasum/reference/RNAsum-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"RNAsum: A Robust Tool for Performing Transcriptome Profiling on Cancer Data — RNAsum-package","text":"Maintainer: Sehrish Kanwal kanwals@unimelb.edu.au (ORCID) Authors: Jacek Marzec jacek.marzec@unimelb.edu.au","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Arriba PDF File — arriba_pdf_read","title":"Read Arriba PDF File — arriba_pdf_read","text":"Reads PDF output Arriba containing one fusion plot per page converts page separate PNG file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Arriba PDF File — arriba_pdf_read","text":"","code":"arriba_pdf_read(pdf = NULL, fusions = NULL, outdir = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Arriba PDF File — arriba_pdf_read","text":"pdf Output PDF file Arriba. fusions Tibble fusions Arriba. outdir Directory write output PNGs .","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Arriba PDF File — arriba_pdf_read","text":"Tibble paths created PNG images clean names. PDF (required params) NULL, returns NULL.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_pdf_read.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Arriba PDF File — arriba_pdf_read","text":"","code":"pdf <- system.file(\"rawdata/test_data/dragen/arriba/fusions.pdf\", package = \"RNAsum\") tsv <- system.file(\"rawdata/test_data/dragen/arriba/fusions.tsv\", package = \"RNAsum\") fusions <- arriba_tsv_read(tsv) (pngs <- arriba_pdf_read(pdf, fusions, tempdir())) #> # A tibble: 4 × 2 #>   nm                                                                 png         #>   <chr>                                                              <chr>       #> 1 EP300.AS1__XRCC6_chr22.41195482_chr22.41636113                     /tmp/RtmpF… #> 2 LAPTM4A__AC098828.3_chr2.20051410_chr2.20064511                    /tmp/RtmpF… #> 3 FNIP1__AC112492.1.83716..DCAF8L1.218._chr5.131642783_chrX.27977775 /tmp/RtmpF… #> 4 ZFP64__MORC2_chr20.52096811_chr22.30963497                         /tmp/RtmpF…"},{"path":"https://umccr.github.io/rnasum/reference/arriba_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process Arriba Fusions — arriba_process","title":"Process Arriba Fusions — arriba_process","text":"Process Arriba Fusions","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process Arriba Fusions — arriba_process","text":"","code":"arriba_process(arriba.fusions, known_translocations, genes_cancer)"},{"path":"https://umccr.github.io/rnasum/reference/arriba_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process Arriba Fusions — arriba_process","text":"arriba.fusions Parsed tibble Arriba fusions. known_translocations Tibble known translocations. genes_cancer Character vector cancer genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process Arriba Fusions — arriba_process","text":"Tibble post-processed Arriba fusion calls.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_summary_write.html","id":null,"dir":"Reference","previous_headings":"","what":"Write Arriba Fusion Summary — arriba_summary_write","title":"Write Arriba Fusion Summary — arriba_summary_write","text":"Writes Arriba fusion summary information (gene1__gene2_bp1_bp2).","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_summary_write.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write Arriba Fusion Summary — arriba_summary_write","text":"","code":"arriba_summary_write(x, file)"},{"path":"https://umccr.github.io/rnasum/reference/arriba_summary_write.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write Arriba Fusion Summary — arriba_summary_write","text":"x Tibble Arriba fusions NULL. file File write summary info .","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_summary_write.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write Arriba Fusion Summary — arriba_summary_write","text":"input invisibly.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Arriba TSV File — arriba_tsv_read","title":"Read Arriba TSV File — arriba_tsv_read","text":"Reads TSV file output Arriba.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Arriba TSV File — arriba_tsv_read","text":"","code":"arriba_tsv_read(x = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Arriba TSV File — arriba_tsv_read","text":"x Path Arriba TSV file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Arriba TSV File — arriba_tsv_read","text":"tibble contents input TSV file, NULL input NULL TSV data rows.","code":""},{"path":"https://umccr.github.io/rnasum/reference/arriba_tsv_read.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Arriba TSV File — arriba_tsv_read","text":"","code":"x <- system.file(\"rawdata/test_data/dragen/arriba/fusions.tsv\", package = \"RNAsum\") (a <- arriba_tsv_read(x)) #> # A tibble: 4 × 30 #>   gene1     gene2      `strand1(gene/fusion)` `strand2(gene/fusion)` breakpoint1 #>   <chr>     <chr>      <chr>                  <chr>                  <chr>       #> 1 EP300-AS1 XRCC6      -/-                    +/+                    chr22:4119… #> 2 LAPTM4A   AC098828.3 -/-                    -/-                    chr2:20051… #> 3 FNIP1     AC112492.… -/-                    ./+                    chr5:13164… #> 4 ZFP64     MORC2      -/-                    -/-                    chr20:5209… #> # ℹ 25 more variables: breakpoint2 <chr>, site1 <chr>, site2 <chr>, type <chr>, #> #   split_reads1 <dbl>, split_reads2 <dbl>, discordant_mates <dbl>, #> #   coverage1 <dbl>, coverage2 <dbl>, confidence <chr>, reading_frame <chr>, #> #   tags <chr>, retained_protein_domains <chr>, #> #   closest_genomic_breakpoint1 <chr>, closest_genomic_breakpoint2 <chr>, #> #   gene_id1 <chr>, gene_id2 <chr>, transcript_id1 <chr>, transcript_id2 <chr>, #> #   direction1 <chr>, direction2 <chr>, filters <chr>, …"},{"path":"https://umccr.github.io/rnasum/reference/barPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate bar-plot for selected genes — barPlot","title":"Generate bar-plot for selected genes — barPlot","text":"Generates bar-plot selected genes, highlighting samples interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/barPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate bar-plot for selected genes — barPlot","text":"","code":"barPlot(   gene,   data,   targets,   y_title = \"Counts\",   sampleName,   ext_cancer,   int_cancer,   add_cancer = NULL )"},{"path":"https://umccr.github.io/rnasum/reference/barPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate bar-plot for selected genes — barPlot","text":"gene User defined gene. data Input data. targets Targets. y_title Title y-axis. sampleName Sample name. ext_cancer External cancer group. int_cancer Internal cancer group. add_cancer Used reordering groups.","code":""},{"path":"https://umccr.github.io/rnasum/reference/barPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate bar-plot for selected genes — barPlot","text":"Bar-plot selected genes, highlighting samples interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cdfPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate CDF plot for selected gene — cdfPlot","title":"Generate CDF plot for selected gene — cdfPlot","text":"Generates cumulative distribution function (CDF) plot selected gene. option \"addBoxPlot\" = TRUE, generate additional boxplot show data variance selected gene individual groups","code":""},{"path":"https://umccr.github.io/rnasum/reference/cdfPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate CDF plot for selected gene — cdfPlot","text":"","code":"cdfPlot(   gene,   data,   targets,   sampleName,   int_cancer,   ext_cancer,   comp_cancer,   add_cancer = NULL,   addBoxPlot = FALSE,   scaling = \"gene-wise\",   report_dir )"},{"path":"https://umccr.github.io/rnasum/reference/cdfPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate CDF plot for selected gene — cdfPlot","text":"gene Gene interest. data Input data. targets Target data set. sampleName Sample name. int_cancer Internal cancer group. ext_cancer External cancer group. comp_cancer Complete cancer group. add_cancer Used reordering groups. addBoxPlot Add boc plot (boolean). scaling Gene-wise sample-wise. report_dir Output directory.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cdfPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate CDF plot for selected gene — cdfPlot","text":"Cumulative distribution function (CDF) plot selected gene.","code":""},{"path":"https://umccr.github.io/rnasum/reference/civicDrugTable.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate table with drugs targeting selected set of genes — civicDrugTable","title":"Generate table with drugs targeting selected set of genes — civicDrugTable","text":"Generates table drugs targeting selected set genes using info CIViC database (https://civicdb.org/).","code":""},{"path":"https://umccr.github.io/rnasum/reference/civicDrugTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate table with drugs targeting selected set of genes — civicDrugTable","text":"","code":"civicDrugTable(   genes,   civic_var_summaries,   civic_clin_evid,   evid_type = \"Predictive\",   var_type = NULL )"},{"path":"https://umccr.github.io/rnasum/reference/civicDrugTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate table with drugs targeting selected set of genes — civicDrugTable","text":"genes Genes interest. civic_var_summaries CIViC variant summaries. civic_clin_evid CIViC clinical evidence. evid_type Evidence type. var_type Variant type.","code":""},{"path":"https://umccr.github.io/rnasum/reference/civicDrugTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate table with drugs targeting selected set of genes — civicDrugTable","text":"Table drugs targeting selected set genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cn_subset.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy Number Subset Table — cn_subset","title":"Copy Number Subset Table — cn_subset","text":"Copy Number Subset Table","code":""},{"path":"https://umccr.github.io/rnasum/reference/cn_subset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy Number Subset Table — cn_subset","text":"","code":"cn_subset(gene.mut = NULL, cn_data, expr_data.z, expr_data.perc)"},{"path":"https://umccr.github.io/rnasum/reference/cn_subset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy Number Subset Table — cn_subset","text":"gene.mut Tibble gene alterations, PCGR run. cn_data Tibble gene MeanCopyNumber expr_data.z Tibble SYMBOL z-score expr values. expr_data.perc Tibble SYMBOL percentile expr values.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cn_subset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy Number Subset Table — cn_subset","text":"tibble Gene, CN, Diff_Perc, Diff_Z_score, Alterations PCGR run.","code":""},{"path":"https://umccr.github.io/rnasum/reference/combineDatasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine sample expression profile with reference datasets — combineDatasets","title":"Combine sample expression profile with reference datasets — combineDatasets","text":"Combines sample expression profile reference datasets. Outputs vector first element containing merged data second element containing merged targets info","code":""},{"path":"https://umccr.github.io/rnasum/reference/combineDatasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine sample expression profile with reference datasets — combineDatasets","text":"","code":"combineDatasets(sample_name, sample_counts, ref_data, report_dir)"},{"path":"https://umccr.github.io/rnasum/reference/combineDatasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine sample expression profile with reference datasets — combineDatasets","text":"sample_name Sample name. sample_counts Sample counts. ref_data Reference data. report_dir Report directory.","code":""},{"path":"https://umccr.github.io/rnasum/reference/combineDatasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine sample expression profile with reference datasets — combineDatasets","text":"Combined sample expression profile reference datasets.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cumsum_ordered.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate cumulative sum — cumsum_ordered","title":"Calculate cumulative sum — cumsum_ordered","text":"Calculating cumulative sum keeping original data order.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cumsum_ordered.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate cumulative sum — cumsum_ordered","text":"","code":"cumsum_ordered(x)"},{"path":"https://umccr.github.io/rnasum/reference/cumsum_ordered.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate cumulative sum — cumsum_ordered","text":"x Input.","code":""},{"path":"https://umccr.github.io/rnasum/reference/cumsum_ordered.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate cumulative sum — cumsum_ordered","text":"Cumulative sum keeping order input data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/densityPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate density and expression distribution plots for selected gene — densityPlot","title":"Generate density and expression distribution plots for selected gene — densityPlot","text":"Generate density expression distribution plots selected gene, highlighting samples interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/densityPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate density and expression distribution plots for selected gene — densityPlot","text":"","code":"densityPlot(   gene,   data,   main_title,   x_title,   sampleName,   distributions = NULL,   scaling = \"gene-wise\" )"},{"path":"https://umccr.github.io/rnasum/reference/densityPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate density and expression distribution plots for selected gene — densityPlot","text":"gene Selected gene. data Input data. main_title Main title. x_title X-axis title. sampleName Sample name. distributions Distributions interest. scaling Scaling.","code":""},{"path":"https://umccr.github.io/rnasum/reference/densityPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate density and expression distribution plots for selected gene — densityPlot","text":"Density expression distribution plots selected gene.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process DRAGEN Fusions — dragen_fusions_process","title":"Process DRAGEN Fusions — dragen_fusions_process","text":"Process DRAGEN Fusions","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process DRAGEN Fusions — dragen_fusions_process","text":"","code":"dragen_fusions_process(dragen.fusions, known_translocations, genes_cancer)"},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process DRAGEN Fusions — dragen_fusions_process","text":"dragen.fusions Parsed tibble DRAGEN fusions. known_translocations Tibble known translocations. genes_cancer Character vector cancer genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process DRAGEN Fusions — dragen_fusions_process","text":"Tibble post-processed DRAGEN fusion calls.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read DRAGEN Fusions — dragen_fusions_read","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"Reads fusion_candidates.final file output DRAGEN.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"","code":"dragen_fusions_read(x = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"x Path fusion_candidates.final file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"tibble contents input TSV file, NULL input NULL TSV data rows.","code":""},{"path":"https://umccr.github.io/rnasum/reference/dragen_fusions_read.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read DRAGEN Fusions — dragen_fusions_read","text":"","code":"x <- system.file(\"rawdata/test_data/dragen\",   \"test_sample_WTS.fusion_candidates.final\",   package = \"RNAsum\" ) (a <- dragen_fusions_read(x)) #> # A tibble: 2 × 15 #>   gene1 gene2   Score LeftBreakpoint RightBreakpoint Gene1Location Gene2Location #>   <chr> <chr>   <dbl> <chr>          <chr>           <chr>         <chr>         #> 1 ATAD2 FBXO32  0.966 chr8:12338052… chr8:123534814… IntactExon    IntactExon    #> 2 NRIP1 AF1275… 0.658 chr21:1506474… chr21:14857708… IntactExon    IntactExon;I… #> # ℹ 8 more variables: Gene1Sense <chr>, Gene2Sense <chr>, Gene1Id <chr>, #> #   Gene2Id <chr>, NumSplitReads <dbl>, NumSoftClippedReads <dbl>, #> #   NumPairedReads <dbl>, ReadNames <chr>"},{"path":"https://umccr.github.io/rnasum/reference/empty_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Empty Tibble Given Column Names — empty_tbl","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"https://stackoverflow.com//62535671/2169986. Useful handling edge cases empty data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/empty_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"","code":"empty_tbl(cnames, ctypes = readr::cols(.default = \"c\"))"},{"path":"https://umccr.github.io/rnasum/reference/empty_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"cnames Character vector column names use. ctypes Character vector column types corresponding cnames.","code":""},{"path":"https://umccr.github.io/rnasum/reference/empty_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"tibble 0 rows given column names.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupStats_groupWise.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","title":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","text":"Calculates group-wise median, sd, quantiles cumulative fractions expression data specific sample group.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupStats_groupWise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","text":"","code":"exprGroupStats_groupWise(data, targets, target)"},{"path":"https://umccr.github.io/rnasum/reference/exprGroupStats_groupWise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","text":"data Input data. targets Target groups. target Defined biological group.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupStats_groupWise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate group-wise median, standard deviation, quantiles and cumulative fractions. — exprGroupStats_groupWise","text":"Group-wise median, standard deviation, quantiles cumulative fractions expression data specific sample group.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupsStats_geneWise.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","title":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","text":"Calculates gene-wise median, sd, quantiles cumulative fractions expression data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupsStats_geneWise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","text":"","code":"exprGroupsStats_geneWise(data, targets)"},{"path":"https://umccr.github.io/rnasum/reference/exprGroupsStats_geneWise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","text":"data input data. targets Target groups","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprGroupsStats_geneWise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data — exprGroupsStats_geneWise","text":"Gene-wise median, standard deviation, quantiles cumulative fractions expression data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprTable.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate table with coloured cells indicating expression values for selected genes — exprTable","title":"Generate table with coloured cells indicating expression values for selected genes — exprTable","text":"Generates table coloured cells indicating expression values selected genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate table with coloured cells indicating expression values for selected genes — exprTable","text":"","code":"exprTable(   data = NULL,   genes = NULL,   keep_all = FALSE,   cn_data = NULL,   sv_data = NULL,   cn_decrease = TRUE,   targets,   sampleName,   int_cancer,   ext_cancer,   comp_cancer,   add_cancer = NULL,   genes_annot = NULL,   oncokb_annot = NULL,   cancer_genes = NULL,   mut_annot = NULL,   fusion_genes = NULL,   type = \"z\",   scaling = \"gene-wise\",   civic_clin_evid = NULL )"},{"path":"https://umccr.github.io/rnasum/reference/exprTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate table with coloured cells indicating expression values for selected genes — exprTable","text":"data Input data. genes Selected genes. keep_all keep rows cn_data Copy number data. sv_data SV data. cn_decrease Order CN data. targets Target groups. sampleName Sample name. int_cancer Internal cancer group. ext_cancer External cancer group. comp_cancer Complete cancer group. add_cancer Additonal cancer type. genes_annot Geners annotation. oncokb_annot OncoKb annotation. cancer_genes Cancer genes. mut_annot Mutation annotation. fusion_genes Fusion genes. type Type. scaling Scaling civic_clin_evid civic_clin_evid tibble reference genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/exprTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate table with coloured cells indicating expression values for selected genes — exprTable","text":"Table coloured cells indicating expression values selected genes","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate Fusions with Ensembl Coordinates — fusions_annot","title":"Annotate Fusions with Ensembl Coordinates — fusions_annot","text":"Annotate Fusions Ensembl Coordinates","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate Fusions with Ensembl Coordinates — fusions_annot","text":"","code":"fusions_annot(fusions, gene_ann)"},{"path":"https://umccr.github.io/rnasum/reference/fusions_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate Fusions with Ensembl Coordinates — fusions_annot","text":"fusions Tibble DRAGEN Arriba fusions. gene_ann Dataframe gene annotations.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotate Fusions with Ensembl Coordinates — fusions_annot","text":"Tibble annotated genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_preprocess.html","id":null,"dir":"Reference","previous_headings":"","what":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","title":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","text":"Pre-Process Arriba DRAGEN Fusions","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_preprocess.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","text":"","code":"fusions_preprocess(d, known_translocations, genes_cancer)"},{"path":"https://umccr.github.io/rnasum/reference/fusions_preprocess.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","text":"d Parsed tibble Arriba DRAGEN fusions. known_translocations Tibble known translocations. genes_cancer Character vector cancer genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_preprocess.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pre-Process Arriba or DRAGEN Fusions — fusions_preprocess","text":"Tibble post-processed fusion calls.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","title":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","text":"Get Arriba/DRAGEN Fusions Summary","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","text":"","code":"fusions_summary(tbl = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/fusions_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","text":"tbl Tibble fusions columns 'gene1' 'gene2'.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Arriba/DRAGEN Fusions Summary — fusions_summary","text":"Character vector 'gene1' 'gene2' genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Fusions Table Display — fusions_table","title":"Fusions Table Display — fusions_table","text":"Fusions Table Display","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fusions Table Display — fusions_table","text":"","code":"fusions_table(fusions)"},{"path":"https://umccr.github.io/rnasum/reference/fusions_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fusions Table Display — fusions_table","text":"fusions Tibble fusions.","code":""},{"path":"https://umccr.github.io/rnasum/reference/fusions_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fusions Table Display — fusions_table","text":"DT object.","code":""},{"path":"https://umccr.github.io/rnasum/reference/genes_pcgr_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Mutated Genes from PCGR — genes_pcgr_summary","title":"Get Mutated Genes from PCGR — genes_pcgr_summary","text":"Get Mutated Genes PCGR","code":""},{"path":"https://umccr.github.io/rnasum/reference/genes_pcgr_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Mutated Genes from PCGR — genes_pcgr_summary","text":"","code":"genes_pcgr_summary(pcgr_tbl, tiers = c(1:4), splice_vars = TRUE)"},{"path":"https://umccr.github.io/rnasum/reference/genes_pcgr_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Mutated Genes from PCGR — genes_pcgr_summary","text":"pcgr_tbl Parsed PCGR TSV tibble. tiers PCGR tiers keep. Default: 1, 2, 3, 4. splice_vars Include non-coding splice region variants reported PCGR?","code":""},{"path":"https://umccr.github.io/rnasum/reference/genes_pcgr_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Mutated Genes from PCGR — genes_pcgr_summary","text":"Character vector genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/getColours.html","id":null,"dir":"Reference","previous_headings":"","what":"Assign colours to different elements — getColours","title":"Assign colours to different elements — getColours","text":"Assigns colours different elements.","code":""},{"path":"https://umccr.github.io/rnasum/reference/getColours.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Assign colours to different elements — getColours","text":"","code":"getColours(elements)"},{"path":"https://umccr.github.io/rnasum/reference/getColours.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Assign colours to different elements — getColours","text":"elements Elements interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/getColours.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Assign colours to different elements — getColours","text":"Colour assignment different elements","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Reference Data File Paths — get_refdata","title":"Get Reference Data File Paths — get_refdata","text":"Get list paths internal external reference data, based selected dataset name.","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Reference Data File Paths — get_refdata","text":"","code":"get_refdata(dataset)"},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Reference Data File Paths — get_refdata","text":"dataset Reference RNAsum dataset interest.","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Reference Data File Paths — get_refdata","text":"List paths internal external reference datasets (Counts, Targets Name).","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refdata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Reference Data File Paths — get_refdata","text":"","code":"x <- get_refdata(dataset = \"TEST\")"},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Reference Genes — get_refgenes","title":"Get Reference Genes — get_refgenes","text":"Get list reference genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Reference Genes — get_refgenes","text":"","code":"get_refgenes(p)"},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Reference Genes — get_refgenes","text":"p RNAsum params list.","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Reference Genes — get_refgenes","text":"List tibbles corresponding cancer, oncokb, immune hrd genes","code":""},{"path":"https://umccr.github.io/rnasum/reference/get_refgenes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Reference Genes — get_refgenes","text":"","code":"p <- list(   genes_cancer = system.file(\"extdata/genes/umccr_cancer_genes.2019-03-20.tsv.gz\",     package = \"RNAsum.data\"   ),   genes_oncokb = system.file(     \"extdata/OncoKB/CancerGenesList.txt.gz\",     package = \"RNAsum.data\"   ),   civic_var_summaries = system.file(     \"extdata/CIViC/01-Oct-2018-VariantSummaries.tsv.gz\",     package = \"RNAsum.data\"   ) ) x <- get_refgenes(p)"},{"path":"https://umccr.github.io/rnasum/reference/glanceExprPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","title":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","text":"Generates boxplot presenting expression profiles selected set genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/glanceExprPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","text":"","code":"glanceExprPlot(   genes,   data,   targets,   sampleName,   int_cancer,   ext_cancer,   comp_cancer,   add_cancer = NULL,   hexcode,   type = \"z\",   sort = \"diff\",   scaling = \"gene-wise\",   report_dir )"},{"path":"https://umccr.github.io/rnasum/reference/glanceExprPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","text":"genes Genes interest. data Input data. targets Target groups. sampleName Sample name. int_cancer Internal cancer group. ext_cancer External cancer group. comp_cancer Complete cancer group. add_cancer Addtional cancer type. hexcode Hexcode. type Type expression values. sort Sort order. scaling Scaling type. report_dir Reprot directory.","code":""},{"path":"https://umccr.github.io/rnasum/reference/glanceExprPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate boxplot presenting expression profiles for selected set of genes — glanceExprPlot","text":"Boxplot presenting expression profiles selected set genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/immune_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Immune Gene Summary — immune_summary","title":"Get Immune Gene Summary — immune_summary","text":"Get Immune Gene Summary","code":""},{"path":"https://umccr.github.io/rnasum/reference/immune_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Immune Gene Summary — immune_summary","text":"","code":"immune_summary(tbl_imarkers, tbl_igram = NULL, igram_param = TRUE)"},{"path":"https://umccr.github.io/rnasum/reference/immune_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Immune Gene Summary — immune_summary","text":"tbl_imarkers Tibble immune response marker genes. tbl_igram Tibble immunogram genes. igram_param Immunogram inclusion TRUE/FALSE parameter.","code":""},{"path":"https://umccr.github.io/rnasum/reference/immune_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Immune Gene Summary — immune_summary","text":"Character vector genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_trans.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Known Translocations — known_trans","title":"Get Known Translocations — known_trans","text":"Flag known fusions based info : FusionGDB (https://ccsm.uth.edu/FusionGDB) Cancer Biomarkers database (CGI) (https://www.cancergenomeinterpreter.org/biomarkers)","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_trans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Known Translocations — known_trans","text":"","code":"known_trans(kt_fusiongdb, kt_cgi)"},{"path":"https://umccr.github.io/rnasum/reference/known_trans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Known Translocations — known_trans","text":"kt_fusiongdb FusionGDB parsed tibble. kt_cgi CGI parsed tibble.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_trans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Known Translocations — known_trans","text":"Tibble known translocations.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_translocations_cgi_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process CGI Known Translocations — known_translocations_cgi_process","title":"Process CGI Known Translocations — known_translocations_cgi_process","text":"Processes parsed CGI known translocations tibble, removing duplicated translocations different source.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_translocations_cgi_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process CGI Known Translocations — known_translocations_cgi_process","text":"","code":"known_translocations_cgi_process(kt_cgi)"},{"path":"https://umccr.github.io/rnasum/reference/known_translocations_cgi_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process CGI Known Translocations — known_translocations_cgi_process","text":"kt_cgi Parsed CGI tibble.","code":""},{"path":"https://umccr.github.io/rnasum/reference/known_translocations_cgi_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process CGI Known Translocations — known_translocations_cgi_process","text":"Tibble dups removed.","code":""},{"path":"https://umccr.github.io/rnasum/reference/manta_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process Manta Object — manta_process","title":"Process Manta Object — manta_process","text":"Process Manta Object","code":""},{"path":"https://umccr.github.io/rnasum/reference/manta_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process Manta Object — manta_process","text":"","code":"manta_process(manta_tsv_obj)"},{"path":"https://umccr.github.io/rnasum/reference/manta_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process Manta Object — manta_process","text":"manta_tsv_obj Manta list object read via gpgr::process_sv.","code":""},{"path":"https://umccr.github.io/rnasum/reference/manta_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process Manta Object — manta_process","text":"List : total Manta (unmelted) variants tibble melted variants genes involved multi-gene events","code":""},{"path":"https://umccr.github.io/rnasum/reference/mutCNexprPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","title":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","text":"Generates scatterplot per-gene expression values (y-axis), CN values (x-axis) mutation status info (colours), provided","code":""},{"path":"https://umccr.github.io/rnasum/reference/mutCNexprPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","text":"","code":"mutCNexprPlot(   data,   alt_data = FALSE,   cn_bottom = cn_bottom,   cn_top = cn_top,   comp_cancer,   type = \"z\",   report_dir )"},{"path":"https://umccr.github.io/rnasum/reference/mutCNexprPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","text":"data Input data. alt_data Boolean (Generates scatterplot per-gene expression values (y-axis)). cn_bottom Bottom value copy number. cn_top Top value copy number. comp_cancer Complete cancer group. type Type. report_dir Report directory.","code":""},{"path":"https://umccr.github.io/rnasum/reference/mutCNexprPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided — mutCNexprPlot","text":"Scatterplot per-gene expression values (y-axis), CN values (x-axis) mutation status info (colours), provided.","code":""},{"path":"https://umccr.github.io/rnasum/reference/nearest_position.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for nearest value in a vector — nearest_position","title":"Check for nearest value in a vector — nearest_position","text":"Check nearest value vector.","code":""},{"path":"https://umccr.github.io/rnasum/reference/nearest_position.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for nearest value in a vector — nearest_position","text":"","code":"nearest_position(vector, x)"},{"path":"https://umccr.github.io/rnasum/reference/nearest_position.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for nearest value in a vector — nearest_position","text":"vector Input vector x Value search","code":""},{"path":"https://umccr.github.io/rnasum/reference/nearest_position.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check for nearest value in a vector — nearest_position","text":"Nearest value vector","code":""},{"path":"https://umccr.github.io/rnasum/reference/pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform PCA — pca","title":"Perform PCA — pca","text":"Perform PCA. Outputs list dataframe samples colouring info ready plotting.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform PCA — pca","text":"","code":"pca(data, targets, title = \"\", report_dir, suffix = \"\")"},{"path":"https://umccr.github.io/rnasum/reference/pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform PCA — pca","text":"data Input data. targets Target group. title Title. report_dir Report directory. suffix Suffix output file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform PCA — pca","text":"Outputs list data frame samples colouring info ready plotting.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PCGR genes with hits — pcgr_expr","title":"Get PCGR genes with hits — pcgr_expr","text":"Get PCGR genes hits","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PCGR genes with hits — pcgr_expr","text":"","code":"pcgr_expr(pcgr = NULL, expr_data.z, expr_data.perc)"},{"path":"https://umccr.github.io/rnasum/reference/pcgr_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get PCGR genes with hits — pcgr_expr","text":"pcgr Path parsed PCGR tiered TSV tibble available. expr_data.z Tibble gene symbol z-score expr values. expr_data.perc Tibble gene symbol percentile expr values.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PCGR genes with hits — pcgr_expr","text":"List.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"Reads snvs_indels.tiers.tsv file output PCGR.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"","code":"pcgr_tiers_tsv_read(x = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"x Path PCGR snvs_indels.tiers.tsv file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"tibble contents input TSV file, NULL x NULL.","code":""},{"path":"https://umccr.github.io/rnasum/reference/pcgr_tiers_tsv_read.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read PCGR Tiers TSV File — pcgr_tiers_tsv_read","text":"","code":"x <- system.file(   \"rawdata/test_data/umccrised/test_sample_WGS/small_variants\",   \"TEST-somatic.pcgr.snvs_indels.tiers.tsv\",   package = \"RNAsum\" ) (ptsv <- pcgr_tiers_tsv_read(x)) #> # A tibble: 99 × 61 #>    CHROM POS       REF   ALT   GENOMIC_CHANGE    GENOME_VERSION VCF_SAMPLE_ID    #>    <chr> <chr>     <chr> <chr> <chr>             <chr>          <chr>            #>  1 3     179218303 G     A     3:g.179218303G>A  grch38         SBJ02999__PRJ22… #>  2 17    7674894   G     A     17:g.7674894G>A   grch38         SBJ02999__PRJ22… #>  3 13    110715614 C     G     13:g.110715614C>G grch38         SBJ02999__PRJ22… #>  4 13    110719444 G     C     13:g.110719444G>C grch38         SBJ02999__PRJ22… #>  5 8     20250093  C     T     8:g.20250093C>T   grch38         SBJ02999__PRJ22… #>  6 8     13086457  C     T     8:g.13086457C>T   grch38         SBJ02999__PRJ22… #>  7 10    31521795  G     C     10:g.31521795G>C  grch38         SBJ02999__PRJ22… #>  8 9     132927250 G     A     9:g.132927250G>A  grch38         SBJ02999__PRJ22… #>  9 3     47121452  G     A     3:g.47121452G>A   grch38         SBJ02999__PRJ22… #> 10 6     117365075 G     C     6:g.117365075G>C  grch38         SBJ02999__PRJ22… #> # ℹ 89 more rows #> # ℹ 54 more variables: VARIANT_CLASS <chr>, SYMBOL <chr>, GENE_NAME <chr>, #> #   CCDS <chr>, CANONICAL <chr>, ENTREZ_ID <chr>, UNIPROT_ID <chr>, #> #   ENSEMBL_TRANSCRIPT_ID <chr>, ENSEMBL_GENE_ID <chr>, REFSEQ_MRNA <chr>, #> #   ONCOSCORE <chr>, ONCOGENE <chr>, TUMOR_SUPPRESSOR <chr>, #> #   ONCOGENE_EVIDENCE <chr>, TUMOR_SUPPRESSOR_EVIDENCE <chr>, #> #   DISGENET_CUI <chr>, DISGENET_TERMS <chr>, CONSEQUENCE <chr>, …"},{"path":"https://umccr.github.io/rnasum/reference/perc_rank.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","title":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","text":"Convert vector numbers corresponding vector percentiles","code":""},{"path":"https://umccr.github.io/rnasum/reference/perc_rank.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","text":"","code":"perc_rank(x)"},{"path":"https://umccr.github.io/rnasum/reference/perc_rank.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","text":"x Input vector","code":""},{"path":"https://umccr.github.io/rnasum/reference/perc_rank.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a vector of numbers into corresponding vector of their percentiles — perc_rank","text":"Vector percentiles","code":""},{"path":"https://umccr.github.io/rnasum/reference/prepare2write.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare object to write into a file — prepare2write","title":"Prepare object to write into a file — prepare2write","text":"Prepare object write file","code":""},{"path":"https://umccr.github.io/rnasum/reference/prepare2write.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare object to write into a file — prepare2write","text":"","code":"prepare2write(x)"},{"path":"https://umccr.github.io/rnasum/reference/prepare2write.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare object to write into a file — prepare2write","text":"x Input object.","code":""},{"path":"https://umccr.github.io/rnasum/reference/prepare2write.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare object to write into a file — prepare2write","text":"Object writing file.","code":""},{"path":"https://umccr.github.io/rnasum/reference/purple_cnv_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PURPLE CNV Summary — purple_cnv_summary","title":"Get PURPLE CNV Summary — purple_cnv_summary","text":"Get PURPLE CNV Summary","code":""},{"path":"https://umccr.github.io/rnasum/reference/purple_cnv_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PURPLE CNV Summary — purple_cnv_summary","text":"","code":"purple_cnv_summary(tbl, cancer_genes_symbol, cn_bottom, cn_top)"},{"path":"https://umccr.github.io/rnasum/reference/purple_cnv_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get PURPLE CNV Summary — purple_cnv_summary","text":"tbl PURPLE gene CNV tibble cancer_genes_symbol Character vector gene symbols filter . cn_bottom CN threshold value classify genes within lost regions. cn_top CN threshold value classify genes within gained regions.","code":""},{"path":"https://umccr.github.io/rnasum/reference/purple_cnv_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PURPLE CNV Summary — purple_cnv_summary","text":"List genes, top bottom copy number thresholds.","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_cyto_info38.html","id":null,"dir":"Reference","previous_headings":"","what":"RCircos HG38 CytoBandIdeogram Object — rcircos_cyto_info38","title":"RCircos HG38 CytoBandIdeogram Object — rcircos_cyto_info38","text":"RCircos HG38 CytoBandIdeogram Object","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_cyto_info38.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RCircos HG38 CytoBandIdeogram Object — rcircos_cyto_info38","text":"","code":"rcircos_cyto_info38()"},{"path":"https://umccr.github.io/rnasum/reference/rcircos_cyto_info38.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"RCircos HG38 CytoBandIdeogram Object — rcircos_cyto_info38","text":"dataframe hg38 cytoband/ideogram information RCircos.","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"RCircos Plot — rcircos_plot","title":"RCircos Plot — rcircos_plot","text":"RCircos Plot","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RCircos Plot — rcircos_plot","text":"","code":"rcircos_plot(df_circos, df_circos_pairs, cyto.info)"},{"path":"https://umccr.github.io/rnasum/reference/rcircos_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RCircos Plot — rcircos_plot","text":"df_circos Dataframe 4 columns: Chromosome, chromStart, chromEnd, Gene. df_circos_pairs Dataframe 3 columns fusion mate: Chromosome, chromStart chromEnd geneA geneB. cyto.info dataframe hg38 cytoband/ideogram information RCircos.","code":""},{"path":"https://umccr.github.io/rnasum/reference/rcircos_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"RCircos Plot — rcircos_plot","text":"RCircos plot object.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Sample Data — read_sample_data","title":"Read Sample Data — read_sample_data","text":"Reads sample data, including Arriba fusions, Arriba plots, Salmon counts, DRAGEN fusions.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Sample Data — read_sample_data","text":"","code":"read_sample_data(p, results_dir, tx2gene = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Sample Data — read_sample_data","text":"p RNAsum params list. results_dir Directory output extracted Arriba PNGs (created automatically already exist). tx2gene data.frame tx_name gene_id columns. Required salmon. See tximport::tximport.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Sample Data — read_sample_data","text":"list input sample data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_sample_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Sample Data — read_sample_data","text":"","code":"p <- list(   dragen_rnaseq = system.file(\"rawdata/test_data/dragen\", package = \"RNAsum\"),   arriba_pdf = system.file(\"rawdata/test_data/dragen/arriba/fusions.pdf\", package = \"RNAsum\"),   arriba_tsv = system.file(\"rawdata/test_data/dragen/arriba/fusions.tsv\", package = \"RNAsum\"),   dragen_fusions = system.file(     \"rawdata/test_data/dragen/test_sample_WTS.fusion_candidates.final\",     package = \"RNAsum\"   ),   umccrise = system.file(     \"rawdata/test_data/umccrised/test_sample_WGS\",     package = \"RNAsum\"   ),   manta_tsv = system.file(     \"rawdata/test_data/umccrised/test_sample_WGS/structural/manta.tsv\",     package = \"RNAsum\"   ) ) res <- read_sample_data(p, tempdir())"},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Read WGS Data — read_wgs_data","title":"Read WGS Data — read_wgs_data","text":"Reads WGS data, including PCGR tiers.tsv, PURPLE cnv.gene.tsv, Manta manta.tsv. file path specified RNAsum params valid, returned. fallback, umccrise directory param specified, attempt detect file pattern .","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read WGS Data — read_wgs_data","text":"","code":"read_wgs_data(p)"},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read WGS Data — read_wgs_data","text":"p RNAsum params list.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read WGS Data — read_wgs_data","text":"list input sample data.","code":""},{"path":"https://umccr.github.io/rnasum/reference/read_wgs_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read WGS Data — read_wgs_data","text":"","code":"p <- list(   umccrise = system.file(\"rawdata/test_data/umccrised/test_sample_WGS\", package = \"RNAsum\"),   pcgr_tiers_tsv = system.file(     \"rawdata/test_data/umccrised/test_sample_WGS/small_variants\",     \"TEST-somatic.pcgr.snvs_indels.tiers.tsv\",     package = \"RNAsum\"   ),   manta_tsv = system.file(     \"rawdata/test_data/umccrised/test_sample_WGS/structural/TEST-prioritize-manta.tsv\",     package = \"RNAsum\"   ) ) (res <- read_wgs_data(p)) #> $pcgr_tiers_tsv #> # A tibble: 99 × 61 #>    CHROM POS       REF   ALT   GENOMIC_CHANGE    GENOME_VERSION VCF_SAMPLE_ID    #>    <chr> <chr>     <chr> <chr> <chr>             <chr>          <chr>            #>  1 3     179218303 G     A     3:g.179218303G>A  grch38         SBJ02999__PRJ22… #>  2 17    7674894   G     A     17:g.7674894G>A   grch38         SBJ02999__PRJ22… #>  3 13    110715614 C     G     13:g.110715614C>G grch38         SBJ02999__PRJ22… #>  4 13    110719444 G     C     13:g.110719444G>C grch38         SBJ02999__PRJ22… #>  5 8     20250093  C     T     8:g.20250093C>T   grch38         SBJ02999__PRJ22… #>  6 8     13086457  C     T     8:g.13086457C>T   grch38         SBJ02999__PRJ22… #>  7 10    31521795  G     C     10:g.31521795G>C  grch38         SBJ02999__PRJ22… #>  8 9     132927250 G     A     9:g.132927250G>A  grch38         SBJ02999__PRJ22… #>  9 3     47121452  G     A     3:g.47121452G>A   grch38         SBJ02999__PRJ22… #> 10 6     117365075 G     C     6:g.117365075G>C  grch38         SBJ02999__PRJ22… #> # ℹ 89 more rows #> # ℹ 54 more variables: VARIANT_CLASS <chr>, SYMBOL <chr>, GENE_NAME <chr>, #> #   CCDS <chr>, CANONICAL <chr>, ENTREZ_ID <chr>, UNIPROT_ID <chr>, #> #   ENSEMBL_TRANSCRIPT_ID <chr>, ENSEMBL_GENE_ID <chr>, REFSEQ_MRNA <chr>, #> #   ONCOSCORE <chr>, ONCOGENE <chr>, TUMOR_SUPPRESSOR <chr>, #> #   ONCOGENE_EVIDENCE <chr>, TUMOR_SUPPRESSOR_EVIDENCE <chr>, #> #   DISGENET_CUI <chr>, DISGENET_TERMS <chr>, CONSEQUENCE <chr>, … #>  #> $purple_gene_tsv #> # A tibble: 25,417 × 20 #>    chromosome  start    end gene        minCopyNumber maxCopyNumber unused #>    <chr>       <int>  <int> <chr>               <dbl>         <dbl> <chr>  #>  1 chr1        11869  14409 DDX11L1              1.98          1.98 0      #>  2 chr1        14404  29570 WASH7P               1.98          1.98 0      #>  3 chr1        17369  17436 MIR6859-1            1.98          1.98 0      #>  4 chr1        29554  31097 MIR1302-2HG          1.98          1.98 0      #>  5 chr1        30366  30503 MIR1302-2            1.98          1.98 0      #>  6 chr1        34554  36081 FAM138A              1.98          1.98 0      #>  7 chr1        69091  70008 OR4F5                1.98          1.98 0      #>  8 chr1       185217 195411 FO538757.1           1.98          1.98 0      #>  9 chr1       187891 187958 MIR6859-2            1.98          1.98 0      #> 10 chr1       450740 451678 OR4F29               1.98          1.98 0      #> # ℹ 25,407 more rows #> # ℹ 13 more variables: somaticRegions <dbl>, germlineHomDeletionRegions <dbl>, #> #   germlineHetToHomDeletionRegions <dbl>, transcriptId <chr>, #> #   transcriptVersion <chr>, chromosomeBand <chr>, minRegions <dbl>, #> #   minRegionStart <int>, minRegionEnd <int>, minRegionStartSupport <chr>, #> #   minRegionEndSupport <chr>, minRegionMethod <chr>, #> #   minMinorAlleleCopyNumber <dbl> #>  #> $manta_tsv #> $manta_tsv$unmelted #> # A tibble: 99 × 19 #>    vcfnum  nann TierTop Start         End    Type  BND_ID BND_mate SR_alt PR_alt #>    <chr>  <dbl> <chr>   <chr>         <chr>  <chr> <chr>  <chr>     <int>  <int> #>  1 68         1 4       1:107,176,815 orpha… BND   1      B             7      9 #>  2 69         1 4       1:107,177,428 orpha… BND   2      A            23     26 #>  3 76         1 4       1:114,885,352 orpha… BND   3      A            27     35 #>  4 01         1 4       1:2,652,000   1:NA   PURP… NA     NA           NA     NA #>  5 02         1 4       1:3,614,001   1:NA   PURP… NA     NA           NA     NA #>  6 03         1 4       1:6,593,001   1:NA   PURP… NA     NA           NA     NA #>  7 04         1 4       1:6,908,000   1:NA   PURP… NA     NA           NA     NA #>  8 05         1 4       1:7,714,001   1:NA   PURP… NA     NA           NA     NA #>  9 06         1 4       1:10,615,000  1:NA   PURP… NA     NA           NA     NA #> 10 07         1 4       1:12,123,001  1:NA   PURP… NA     NA           NA     NA #> # ℹ 89 more rows #> # ℹ 9 more variables: SR_PR_sum <int>, SR_PR_ref <chr>, Ploidy <dbl>, #> #   AF_PURPLE <chr>, AF_BPI <chr>, CNC <chr>, CN <chr>, SScore <int>, #> #   annotation <chr> #>  #> $manta_tsv$melted #> # A tibble: 186 × 28 #>    vcfnum  nann TierTop Start         End    Type  BND_ID BND_mate SR_alt PR_alt #>    <chr>  <dbl> <chr>   <chr>         <chr>  <chr> <chr>  <chr>     <int>  <int> #>  1 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  2 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  3 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  4 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  5 62         5 3       1:97,924,845  1:97,… DUP   NA     NA           21     15 #>  6 13         4 3       1:20,551,467  1:20,… DEL   NA     NA           11     21 #>  7 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  8 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #>  9 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #> 10 82        61 3       1:150,364,461 1:150… DUP   NA     NA           18     28 #> # ℹ 176 more rows #> # ℹ 18 more variables: SR_PR_sum <int>, SR_PR_ref <chr>, Ploidy <dbl>, #> #   AF_PURPLE <chr>, AF_BPI <chr>, CNC <chr>, CN <chr>, SScore <int>, #> #   Event <chr>, Effect <chr>, Genes <chr>, Transcript <chr>, Detail <chr>, #> #   Tier <chr>, ntrx <dbl>, ngen <dbl>, neff <dbl>, `Tier (Top)` <glue> #>  #> $manta_tsv$tsv_descr #> # A tibble: 23 × 3 #>    Column             Description                                          Type  #>    <chr>              <chr>                                                <chr> #>  1 caller             Manta SV caller                                      c     #>  2 sample             Tumor sample name                                    c     #>  3 chrom              CHROM column in VCF                                  c     #>  4 start              POS column in VCF                                    i     #>  5 end                INFO/END: End position of the variant described in … i     #>  6 svtype             INFO/SVTYPE: Type of structural variant              c     #>  7 split_read_support FORMAT/SR of tumor sample: Split reads for the ref … c     #>  8 paired_support_PE  FORMAT/PE of tumor sample: ??                        c     #>  9 paired_support_PR  FORMAT/PR of tumor sample: Spanning paired-read sup… c     #> 10 AF_BPI             INFO/BPI_AF: AF at each breakpoint (so AF_BPI1,AF_B… c     #> # ℹ 13 more rows #>  #> $manta_tsv$col_descr #> # A tibble: 30 × 2 #>    Column     Description                                                        #>    <chr>      <chr>                                                              #>  1 nrow       \"Row number that connects variants between tables in same tab set… #>  2 vcfnum     \"Original event row number that connects variants to events.\"      #>  3 TierTop    \"Top priority of the event (from simple_sv_annotation: 1 highest,… #>  4 Tier       \"Priority of the specific event (from simple_sv_annotation: 1 hig… #>  5 Tier (Top) \"Priority of the specific event (Top tier of all event's annotati… #>  6 Chr        \"Chromosome.\"                                                      #>  7 Start      \"Start position as inferred by BPI. For PURPLE-inferred SVs we us… #>  8 End        \"End position. For BNDs = Chr:Start of the mate.Values are inferr… #>  9 ID         \"ID of BND from Manta. For PURPLE-inferred SVs this is PURPLE.\"    #> 10 MATEID     \"ID of BND mate from Manta.\"                                       #> # ℹ 20 more rows #>  #>"},{"path":"https://umccr.github.io/rnasum/reference/rnasum_rmd.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate UMCCR RNAsum Report — rnasum_rmd","title":"Generate UMCCR RNAsum Report — rnasum_rmd","text":"Generates UMCCR RNAsum HTML report. following steps: copy rmd tmp/rnasum.Rmd render rmd inside tmp/ return path output HTML","code":""},{"path":"https://umccr.github.io/rnasum/reference/rnasum_rmd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate UMCCR RNAsum Report — rnasum_rmd","text":"","code":"rnasum_rmd(out_file = NULL, quiet = FALSE, pars)"},{"path":"https://umccr.github.io/rnasum/reference/rnasum_rmd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate UMCCR RNAsum Report — rnasum_rmd","text":"out_file Path output HTML file (needs '.html' suffix). quiet Suppress printing rendering. pars List named parameters override custom params specified within Rmd's YAML front-matter.","code":""},{"path":"https://umccr.github.io/rnasum/reference/rnasum_rmd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate UMCCR RNAsum Report — rnasum_rmd","text":"Path rendered HTML report.","code":""},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Salmon Counts — salmon_counts","title":"Get Salmon Counts — salmon_counts","text":"Get salmon counts via tximport.","code":""},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Salmon Counts — salmon_counts","text":"","code":"salmon_counts(x, tx2gene = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Salmon Counts — salmon_counts","text":"x Path quant.sf file abundances. See tximport::tximport. tx2gene data.frame tx_name gene_id columns. See tximport::tximport.","code":""},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Salmon Counts — salmon_counts","text":"Tibble counts per gene transcript, NULL input params NULL.","code":""},{"path":"https://umccr.github.io/rnasum/reference/salmon_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Salmon Counts — salmon_counts","text":"","code":"x <- system.file(\"rawdata/test_data/dragen/TEST.quant.sf\", package = \"RNAsum\") tx2gene <- NULL (sc <- salmon_counts(x, tx2gene)) # NULL since no tx2gene specified #> NULL"},{"path":"https://umccr.github.io/rnasum/reference/saveWidgetFix.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for saveWidget bug fix — saveWidgetFix","title":"Wrapper for saveWidget bug fix — saveWidgetFix","text":"wrapper saveWidget compensates bug temporary directory widget dependencies deleted - see https://github.com/ramnathv/htmlwidgets/issues/296.","code":""},{"path":"https://umccr.github.io/rnasum/reference/saveWidgetFix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for saveWidget bug fix — saveWidgetFix","text":"","code":"saveWidgetFix(widget, file, selfcontained = TRUE, ...)"},{"path":"https://umccr.github.io/rnasum/reference/saveWidgetFix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for saveWidget bug fix — saveWidgetFix","text":"widget Widget save. file Full path save HTML . selfcontained Whether save HTML single self-contained file (external resources base64 encoded) file external resources placed adjacent directory. ... Additional arguments passed htmlwidgets::saveWidget.","code":""},{"path":"https://umccr.github.io/rnasum/reference/saveWidgetFix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for saveWidget bug fix — saveWidgetFix","text":"Change work dir compensate saveWidget bug","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_kable.html","id":null,"dir":"Reference","previous_headings":"","what":"Session Information Kable — session_info_kable","title":"Session Information Kable — session_info_kable","text":"Session information kables vignettes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_kable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Session Information Kable — session_info_kable","text":"","code":"session_info_kable(pkgs = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/session_info_kable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Session Information Kable — session_info_kable","text":"pkgs Vector R packages display vignette. default returns .","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_kable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Session Information Kable — session_info_kable","text":"list two kables containing information platform specified packages.","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_tbls.html","id":null,"dir":"Reference","previous_headings":"","what":"Session Information Tables — session_info_tbls","title":"Session Information Tables — session_info_tbls","text":"Session information tables.","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_tbls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Session Information Tables — session_info_tbls","text":"","code":"session_info_tbls(pkgs = NULL)"},{"path":"https://umccr.github.io/rnasum/reference/session_info_tbls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Session Information Tables — session_info_tbls","text":"pkgs Vector R packages display vignette. default returns .","code":""},{"path":"https://umccr.github.io/rnasum/reference/session_info_tbls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Session Information Tables — session_info_tbls","text":"list two tibbles containing information platform specified packages.","code":""},{"path":"https://umccr.github.io/rnasum/reference/sv_manta_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Manta SV Summary — sv_manta_summary","title":"Get Manta SV Summary — sv_manta_summary","text":"Get Manta SV Summary","code":""},{"path":"https://umccr.github.io/rnasum/reference/sv_manta_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Manta SV Summary — sv_manta_summary","text":"","code":"sv_manta_summary(tbl)"},{"path":"https://umccr.github.io/rnasum/reference/sv_manta_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Manta SV Summary — sv_manta_summary","text":"tbl Tibble melted SVs umccrise, containing 'Genes' column.","code":""},{"path":"https://umccr.github.io/rnasum/reference/sv_manta_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Manta SV Summary — sv_manta_summary","text":"Character vector Genes.","code":""},{"path":"https://umccr.github.io/rnasum/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://www.tidyverse.org/blog/2019/06/rlang-0-4-0/","code":""},{"path":"https://umccr.github.io/rnasum/reference/tpm_from_rpkm.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate TPM from RPKM — tpm_from_rpkm","title":"Calculate TPM from RPKM — tpm_from_rpkm","text":"Calculate TPM RPKM (http://luisvalesilva.com/datasimple/rna-seq_units.html )","code":""},{"path":"https://umccr.github.io/rnasum/reference/tpm_from_rpkm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate TPM from RPKM — tpm_from_rpkm","text":"","code":"tpm_from_rpkm(x)"},{"path":"https://umccr.github.io/rnasum/reference/tpm_from_rpkm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate TPM from RPKM — tpm_from_rpkm","text":"x RPKM values","code":""},{"path":"https://umccr.github.io/rnasum/reference/tpm_from_rpkm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate TPM from RPKM — tpm_from_rpkm","text":"TPM values","code":""},{"path":"https://umccr.github.io/rnasum/reference/webplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate spider web plots to present immunogram genes — webplot","title":"Generate spider web plots to present immunogram genes — webplot","text":"Generate spider web plots present immunogram genes (http://www.statisticstoproveanything.com/2013/11/spider-web-plots--r.html).","code":""},{"path":"https://umccr.github.io/rnasum/reference/webplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate spider web plots to present immunogram genes — webplot","text":"","code":"webplot(   data,   data.row = NULL,   y.cols = NULL,   main = NULL,   add = F,   col = \"red\",   lty = 1,   scale = T )"},{"path":"https://umccr.github.io/rnasum/reference/webplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate spider web plots to present immunogram genes — webplot","text":"data Dataframe matrix. data.row Row data plot (NULL uses row 1). y.cols Columns interest (NULL selects numeric columns). main Title plot (NULL rowname data). add Whether plot added existing plot. col Color data line lty Lty data line scale Scale.","code":""},{"path":"https://umccr.github.io/rnasum/reference/webplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate spider web plots to present immunogram genes — webplot","text":"Spider web plots present immunogram genes","code":""}]