chord_run: Run CHORD

Description Usage Arguments Value Examples

View source: R/chord.R

Description

Runs CHORD given SNV and SV VCF files. NOTE: make sure you have the BSgenome.Hsapiens.UCSC.hgXX installed.

Usage

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chord_run(
  vcf.snv = NULL,
  vcf.sv = NULL,
  df.sv = NULL,
  sample.name = NULL,
  ref.genome = "hg38",
  sv.caller = "manta",
  outpath = NULL,
  ...
)

Arguments

vcf.snv

Path to VCF containing SNVs and INDELs.

vcf.sv

Path to VCF containing SVs.

df.sv

A data.frame object containing the columns 'SVTYPE' and 'SVLEN' from a Manta SV VCF.

sample.name

Name of sample to use.

ref.genome

Human genome assembly. One of 'hg38' (default), 'hg19' or 'GRCh37'.

sv.caller

manta (default) or gridss.

outpath

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

...

Other arguments to be passed to CHORD::extractSigsChord().

Value

List with extracted signatures and HRD prediction.

Examples

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snv <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
sv <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
chord_res <- chord_run(
  vcf.snv = snv, df.sv = chord_mantavcf2df(sv),
  sample.name = "foo"
)
# chord_res2 <- chord_run(vcf.snv = snv, vcf.sv = sv, sample.name = "foo",
#                         outpath = "nogit/chord_results.json.gz")

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