palimpsest_makeMutypeMatFromVcf: palimpsest_makeMutypeMatFromVcf
In FunGeST/Palimpsest: Package

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

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

`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