hrdetect_prep_snvindel: Prepare VCF with SNVs/INDELs for use with HRDetect

Description Usage Arguments Value Examples

View source: R/hrdetect.R

Description

Prepares VCF with SNVs/INDELs for use with HRDetect.

Usage

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hrdetect_prep_snvindel(
  x,
  nm = NULL,
  genome = "hg38",
  outdir = NULL,
  sigsToUse = c(1, 2, 3, 5, 6, 8, 13, 17, 18, 20, 26, 30)
)

Arguments

x

Path to VCF with SNVs and INDELs.

nm

Sample name.

genome

Human genome version (default: hg38. hg19 means GRCh37).

outdir

Directory to output analysis results.

sigsToUse

COSMIC signatures to use.

Value

List with two elements:

Examples

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x <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
(l <- hrdetect_prep_snvindel(x, nm = "sampleA", outdir = tempdir()))

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