palimpsest_makeMutypeMatFromVcf: palimpsest_makeMutypeMatFromVcf

In FunGeST/Palimpsest: Package

palimpsest_makeMutypeMatFromVcf

Description

Function to create a matrix in mutation type x sample format with either counts or proportions

Usage

palimpsest_makeMutypeMatFromVcf(
  vcf,
  sample.col = "sample",
  mutcat.col = "mutcat3",
  mutypes = c("CA", "CG", "CT", "TA", "TC", "TG"),
  proportion = TRUE
)

Arguments

vcf	vcf data frame containing the mutations
sample.col	Name of column containing sample names
mutcat.col	Name of column containing mutation categories
mutypes	List of categories to be included in the output
proportion	If TRUE, the output matrix will indicate mutation proportions instead of numbers

FunGeST/Palimpsest documentation built on June 2, 2024, 4:21 a.m.