From 7253dae8bc2c6cd95a1ce4cf14a8f4a115934bc2 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sat, 18 Nov 2023 03:42:27 +0000 Subject: [PATCH] Built site for RNAsum: 0.5.0.9000@7cfefce - see https://umccr.github.io/RNAsum/ --- 404.html | 2 +- LICENSE-text.html | 2 +- LICENSE.html | 2 +- articles/development.html | 4 +- articles/index.html | 2 +- articles/report_structure.html | 4 +- articles/tcga_projects_summary.html | 4 +- articles/workflow.html | 4 +- authors.html | 2 +- index.html | 262 +++++++++--------- pkgdown.yml | 4 +- reference/CapStr.html | 2 +- reference/REFERENCE_DATASETS.html | 2 +- reference/RNAsum-package.html | 2 +- reference/arriba_pdf_read.html | 10 +- reference/arriba_process.html | 2 +- reference/arriba_summary_write.html | 2 +- reference/arriba_tsv_read.html | 2 +- reference/barPlot.html | 2 +- reference/cdfPlot.html | 2 +- reference/civicDrugTable.html | 2 +- reference/cn_subset.html | 2 +- reference/combineDatasets.html | 2 +- reference/cumsum_ordered.html | 2 +- reference/densityPlot.html | 2 +- reference/dragen_fusions_process.html | 2 +- reference/dragen_fusions_read.html | 2 +- reference/dragen_mapping_metrics_read.html | 118 ++++++++ reference/empty_tbl.html | 2 +- reference/exprGroupStats_groupWise.html | 2 +- reference/exprGroupsStats_geneWise.html | 2 +- reference/exprTable.html | 2 +- reference/fusions_annot.html | 2 +- reference/fusions_preprocess.html | 2 +- reference/fusions_summary.html | 2 +- reference/fusions_table.html | 2 +- reference/genes_pcgr_summary.html | 2 +- reference/getColours.html | 2 +- reference/get_refdata.html | 2 +- reference/get_refgenes.html | 2 +- reference/glanceExprPlot.html | 2 +- reference/immune_summary.html | 2 +- reference/index.html | 7 +- reference/known_trans.html | 2 +- .../known_translocations_cgi_process.html | 2 +- reference/manta_process.html | 4 +- reference/mutCNexprPlot.html | 2 +- reference/nearest_position.html | 2 +- reference/pca.html | 2 +- reference/pcgr_expr.html | 2 +- reference/pcgr_tiers_tsv_read.html | 2 +- reference/perc_rank.html | 2 +- reference/prepare2write.html | 2 +- reference/purple_cnv_summary.html | 2 +- reference/rcircos_cyto_info38.html | 2 +- reference/rcircos_plot.html | 2 +- reference/read_sample_data.html | 21 +- reference/read_wgs_data.html | 93 ++----- reference/rnasum_rmd.html | 2 +- reference/salmon_counts.html | 4 +- reference/saveWidgetFix.html | 2 +- reference/session_info_kable.html | 2 +- reference/session_info_tbls.html | 2 +- reference/sv_manta_summary.html | 2 +- reference/tidyeval.html | 2 +- reference/tpm_from_rpkm.html | 2 +- reference/webplot.html | 2 +- search.json | 2 +- sitemap.xml | 3 + 69 files changed, 363 insertions(+), 289 deletions(-) create mode 100644 reference/dragen_mapping_metrics_read.html diff --git a/404.html b/404.html index d39069b6..2e2a657d 100644 --- a/404.html +++ b/404.html @@ -24,7 +24,7 @@ RNAsum - 0.4.10 + 0.5.0.9000 + + + + + +
+
+
+

Read DRAGEN Mapping Metrics

+ Source: R/qc_dragen.R +
dragen_mapping_metrics_read.Rd
+
+ +
+

Reads the mapping_metrics.csv file output by DRAGEN.

+
+ +
+

Usage

+ 
dragen_mapping_metrics_read(x = NULL)
+
+ +
+

Arguments

+
x
+

Path to the mapping_metrics.csv file.

+ +
+
+

Value

+ + +

A tibble with the contents of the input TSV file, or NULL if input is NULL or TSV has no data rows.

+
+ +
+

Examples

+ 
x <- system.file("rawdata/test_data/dragen",
+  "test.mapping_metrics.csv",
+  package = "RNAsum"
+)
+(d1 <- dragen_mapping_metrics_read(x))
+#> # A tibble: 113 × 6
+#>    category rg    var                                   var_abbrev   count   pct
+#>    <chr>    <chr> <chr>                                 <chr>        <dbl> <dbl>
+#>  1 summary  TOTAL Total input reads                     reads_tot…  2.40e8 100  
+#>  2 summary  TOTAL Number of duplicate marked reads      reads_num…  0        0  
+#>  3 summary  TOTAL Number of duplicate marked and mate … reads_num… NA       NA  
+#>  4 summary  TOTAL Number of unique reads (excl. duplic… reads_num…  2.40e8 100  
+#>  5 summary  TOTAL Reads with mate sequenced             reads_w_m…  2.40e8 100  
+#>  6 summary  TOTAL Reads without mate sequenced          reads_wo_…  0        0  
+#>  7 summary  TOTAL QC-failed reads                       reads_qcf…  0        0  
+#>  8 summary  TOTAL Mapped reads                          reads_map…  1.69e8  70.3
+#>  9 summary  TOTAL Mapped reads adjusted for filtered m… reads_map…  1.70e8  70.7
+#> 10 summary  TOTAL Mapped reads R1                       reads_map…  8.43e7  70.3
+#> # ℹ 103 more rows
+
+
+
+ + +
+

Developed by Sehrish Kanwal, Jacek Marzec.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/reference/empty_tbl.html b/reference/empty_tbl.html index 36151f1a..2c3e3117 100644 --- a/reference/empty_tbl.html +++ b/reference/empty_tbl.html @@ -12,7 +12,7 @@ RNAsum - 0.4.10 + 0.5.0.9000