hrd_results_tabs: HRDetect and CHORD Summary Table

In umccr/gpgr: Genomics Platform Group Reporting

HRDetect and CHORD Summary Table

Description

Return a summary table with HRDetect and CHORD results.

Usage

hrd_results_tabs(hrdetect_res, chord_res, dragen_res)

Arguments

hrdetect_res	Result from running sigrap::hrdetect_run().
chord_res	Result from running sigrap::chord_run().
dragen_res	Result from running dragen_hrd().

Value

A list with a tibble and a gt_tbl object (see gt::gt()).

Examples

## Not run: 
snv <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
sv <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
cnv <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
nm <- "SampleA"
genome <- "hg38"
snvoutdir <- tempdir()
hrdetect_res <- sigrap::hrdetect_run(nm, snv, sv, cnv, genome, snvoutdir)
chord_res <- sigrap::chord_run(
  vcf.snv = snv, sample.name = nm,
  df.sv = gpgr:::chord_mantavcf2df(sv)
)
dragen_res <- gpgr::dragen_hrd("path/to/sample.hrdscore.csv")
hrd_results_tabs(hrdetect_res = hrdetect_res, chord_res = chord_res, dragen_res = dragen_res)

## End(Not run)

umccr/gpgr documentation built on April 21, 2024, 1:16 a.m.