extractSigsChord: Extract mutation contexts in the format compatible with CHORD

In luannnguyen/CHORD: Classifier of Homologous Recombination Deficiency

Extract mutation contexts in the format compatible with CHORD

Description

This function is a wrapper for the 3 functions from mutSigExtractor: extractSigsSnv(), extractSigsIndel(), extractSigsSv(). Some post-processing is done to produce compatible input for CHORD

Usage

extractSigsChord(
  vcf.snv = NULL,
  vcf.indel = vcf.snv,
  vcf.sv = NULL,
  df.snv = NULL,
  df.indel = df.snv,
  df.sv = NULL,
  sample.name = "sample",
  vcf.filters = list(snv = NA, indel = NA, sv = NA),
  sv.caller = "gridss",
  output.path = NULL,
  ref.genome = mutSigExtractor::DEFAULT_GENOME,
  verbose = F
)

Arguments

vcf.snv	Path to the vcf file containing SNVs
vcf.indel	Path to the vcf file containing indels. By default vcf.indel=vcf.snv
vcf.sv	Path to the vcf file containing SVs
df.snv	A dataframe containing the columns: chrom, pos, ref, alt.
df.indel	A dataframe containing the columns: chrom, pos, ref, alt.
df.sv	A dataframe with the columns: sv_type, sv_len. sv_type can be DEL, DUP, INV, TRA, BND.
sample.name	The name of the sample as a character. Defaults to 'sample' if none is provided.
vcf.filters	A list of in the form list(snv=character(),indel=character(),sv=character()) indicated which variants to keep, corresponding to the values in the vcf FILTER column. NA can be specified for each list item to ignore filtering of a vcf.
sv.caller	SV vcfs are not standardized and therefore need to be parsed differently depending on the caller. Currently supports 'manta' or 'gridss'.
output.path	If a path is specified, the output is written to this path.
ref.genome	A BSgenome reference genome. Default is BSgenome.Hsapiens.UCSC.hg19. If another reference genome is indicated, it will also need to be installed.
verbose	Whether to print progress messages

Value

A 1-row data frame containing the mutational signature contributions

luannnguyen/CHORD documentation built on Aug. 25, 2023, 10:04 a.m.