palimpsest_input: palimpsest_input

In FunGeST/Palimpsest: Package

palimpsest_input

Description

Creates the list of input matrices of the numbers and proportions of each mutation category (of one mutation type, e.g. SBS mutation categories) in each sample.

Usage

palimpsest_input(vcf = NULL, Type = NULL, mutypes = NA)

Arguments

vcf	The input VCF file from which a matrix of mutation categories is to be made.
Type	Mutation type (SBS, DBS, ID or SV).
mutypes	leave blank to use default COSMIC categories (recommeneded), or add your own.

Examples

DBS_input <- palimpsest_input(vcf=vcf, Type = "DBS")

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