palimpsest_addSVcategoriesToVcf: palimpsest_addSVcategoriesToVcf

In FunGeST/Palimpsest: Package

Description

Function to add SV mutation categories to vcf

Usage

palimpsest_addSVcategoriesToVcf(
  sv = sv,
  type.col = "Type",
  sample.col = "Sample",
  CHROM_1.col = "CHROM",
  CHROM_2.col = "CHROM",
  POS_1.col = "POS",
  POS_2.col = "POS",
  resdir = resdir,
  genome_build = "hg19"
)

Arguments

sv	vcf data frame containing the SVs
type.col	SV type description column name in mutation_data ["DEL","DUP","INV"]
sample.col	Sample column name in sv
CHROM_1.col	Start chromosome column name in sv
CHROM_2.col	End chromosome column name in sv
POS_1.col	Start position column name in sv
POS_2.col	End position column name in sv
resdir	Result directory

FunGeST/Palimpsest documentation built on June 10, 2021, 6:35 p.m.