vignettes/development.Rmd
development.Rmd
vignettes/report_structure.Rmd
report_structure.Rmd
vignettes/tcga_projects_summary.Rmd
tcga_projects_summary.Rmd
vignettes/workflow.Rmd
workflow.Rmd
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 +1.0.0 $ rnasum.R --help Usage ===== -/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RNAsum/cli/rnasum.R [options] +/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RNAsum/cli/rnasum.R [options] Options ======= ---arriba_pdf=ARRIBA_PDF - File path of Arriba PDF output +--arriba_dir=ARRIBA_DIR + Directory path to Arriba results containing fusions.pdf and fusions.tsv. ---arriba_tsv=ARRIBA_TSV - File path of Arriba TSV output +--arriba_pdf=ARRIBA_PDF + File path of Arriba PDF output. ---batch_rm=BATCH_RM - Remove batch-associated effects between datasets? [def: TRUE] +--arriba_tsv=ARRIBA_TSV + File path of Arriba TSV output. ---cn_gain=CN_GAIN - CN threshold value to classify genes within gained regions [def: 95] +--batch_rm + Remove batch-associated effects between datasets. ---cn_loss=CN_LOSS - CN threshold value to classify genes within lost regions [def: 5] +--cn_gain=CN_GAIN + CN threshold value to classify genes within gained regions. [def: 95] ---dataset=DATASET - Dataset to be used as external reference cohort [def: PANCAN] +--cn_loss=CN_LOSS + CN threshold value to classify genes within lost regions. [def: 5] ---dataset_name_incl=DATASET_NAME_INCL - Include dataset in report name? [def: FALSE] +--dataset=DATASET + Dataset to be used as external reference cohort. [def: PANCAN] ---dragen_fusions=DRAGEN_FUSIONS - File path to DRAGEN RNA-seq 'fusion_candidates.final' output +--dataset_name_incl + Include dataset in report name. ---drugs=DRUGS - Include drug matching section in report? [def: FALSE] +--dragen_fusions=DRAGEN_FUSIONS + File path to DRAGEN RNA-seq 'fusion_candidates.final' output. ---filter=FILTER - Filter out low expressed genes? [def: TRUE] +--dragen_mapping_metrics=DRAGEN_MAPPING_METRICS + File path to DRAGEN RNA-seq 'mapping_metrics.csv' output. ---hide_code_btn=HIDE_CODE_BTN - Hide "Code" button above code chunks in report? [def: TRUE] +--dragen_wts_dir=DRAGEN_WTS_DIR + Directory path to DRAGEN RNA-seq results. ---immunogram=IMMUNOGRAM - Include immunogram in report? [def: FALSE] +--drugs + Include drug matching section in report. ---log=LOG - Log2 transform data before normalisation? [def: TRUE] +--filter + Filter out low expressed genes. ---manta_tsv=MANTA_TSV - File path to umccrise 'manta.tsv' output +--immunogram + Include immunogram in report. ---norm=NORM - Normalisation method +--log + Log2 transform data before normalisation. ---pcgr_splice_vars=PCGR_SPLICE_VARS - Include non-coding splice region variants reported in PCGR? [def: TRUE] +--manta_tsv=MANTA_TSV + File path to umccrise 'manta.tsv' output. ---pcgr_tier=PCGR_TIER - Tier threshold for reporting variants reported in PCGR [def: 4] +--norm=NORM + Normalisation method. ---pcgr_tiers_tsv=PCGR_TIERS_TSV - File path to PCGR 'snvs_indels.tiers.tsv' output +--pcgr_splice_vars + Include non-coding splice region variants reported in PCGR. ---project=PROJECT - Project name +--pcgr_tier=PCGR_TIER + Tier threshold for reporting variants reported in PCGR. [def: 4] ---purple_gene_tsv=PURPLE_GENE_TSV - File path to PURPLE 'purple.cnv.gene.tsv' output +--pcgr_tiers_tsv=PCGR_TIERS_TSV + File path to PCGR 'snvs_indels.tiers.tsv' output. ---report_dir=REPORT_DIR - Directory path to output report +--project=PROJECT + Project name, used for annotation purposes only. ---salmon=SALMON - File path to salmon 'quant.sf' output +--purple_gene_tsv=PURPLE_GENE_TSV + File path to PURPLE 'purple.cnv.gene.tsv' output. ---sample_name=SAMPLE_NAME - Sample name to be presented in report +--report_dir=REPORT_DIR + Directory path to output report. ---sample_source=SAMPLE_SOURCE - Type of investigated sample [def: -] +--salmon=SALMON + File path to salmon 'quant.genes.sf' output. ---save_tables=SAVE_TABLES - Save interactive summary tables as HTML? [def: TRUE] +--sample_name=SAMPLE_NAME + Sample name to be presented in report. ---scaling=SCALING - Scaling for z-score transformation (gene-wise or group-wise) [def: gene-wise] +--sample_source=SAMPLE_SOURCE + Type of investigated sample. [def: -] ---subject_id=SUBJECT_ID - Subject ID +--save_tables + Save interactive summary tables as HTML. ---top_genes=TOP_GENES - Number of top ranked genes to be presented in report +--scaling=SCALING + Scaling for z-score transformation (gene-wise or group-wise). [def: gene-wise] ---transform=TRANSFORM - Transformation method to be used when converting read counts [def: CPM] +--subject_id=SUBJECT_ID + Subject ID. ---umccrise=UMCCRISE - Directory path of the corresponding WGS-related data +--top_genes=TOP_GENES + Number of top ranked genes to be presented in report. ---help, -h - Show this help message and exit
Note
Human reference genome GRCh38 (Ensembl based annotation version 86) is used for gene annotation by default. GRCh37 is no longer supported.
The results folder contains intermediate files, including plots and tables that are presented in the HTML report.
results
The code of conduct can be accessed here.