hrd_results_tabs: HRDetect and CHORD Summary Table

Description Usage Arguments Value Examples

View source: R/umccrise.R

Description

Return a summary table with HRDetect and CHORD results.

Usage

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hrd_results_tabs(hrdetect_res, chord_res)

Arguments

hrdetect_res

Result from running hrdetect_run().

chord_res

Result from running chord_run().

Value

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

Examples

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## 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 <- hrdetect_run(nm, snv, sv, cnv, genome, snvoutdir)
chord_res <- chord_run(vcf.snv = snv, df.sv = gpgr:::chord_mantavcf2df(sv), sample.name = nm)
hrd_results_tabs(hrdetect_res = hrdetect_res, chord_res = chord_res)

## End(Not run)

umccr/gpgr documentation built on Nov. 25, 2021, 1:15 p.m.