hrdetect_run: Run HRDetect via signature.tools.lib

Description Usage Arguments Value Examples

View source: R/hrdetect.R

Description

Runs HRDetect as described in the signature.tools.lib repository.

Usage

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hrdetect_run(
  nm,
  snvindel_vcf,
  sv_vcf,
  cnv_tsv,
  genome = "hg38",
  snvoutdir = tempdir(),
  sigsToUse = c(1, 2, 3, 5, 6, 8, 13, 17, 18, 20, 26, 30),
  outpath = NULL
)

Arguments

nm

Sample name.

snvindel_vcf

Path to VCF with SNVs and INDELs.

sv_vcf

Path to VCF with SVs.

cnv_tsv

Path to purple.cnv.somatic.tsv file.

genome

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

snvoutdir

Directory to output SNV signature analysis results.

sigsToUse

COSMIC SNV signatures to use.

outpath

File to write HRDetect predictions to on disk (should end in '.gz'). If not specified, results won't be written to disk.

Value

Tibble with sample name and HRD probability in first two columns.

Examples

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snvindel_vcf <- system.file(
  "extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz",
  package = "gpgr"
)
sv_vcf <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
cnv_tsv <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
nm <- "SampleA"
genome <- "hg38"
snvoutdir <- tempdir()
(res <- hrdetect_run(nm, snvindel_vcf, sv_vcf, cnv_tsv, genome, snvoutdir))
# hrdetect_run(nm, snvindel_vcf, sv_vcf, cnv_tsv, genome, snvoutdir,
#              outpath = "nogit/hrdetect_results.json.gz")

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