ICAMS (version 3.0.11)

AddAndCheckDBSClassInVCF: Add and check DBS class in an annotated VCF with the corresponding DBS mutation matrix

Description

Add and check DBS class in an annotated VCF with the corresponding DBS mutation matrix

Usage

AddAndCheckDBSClassInVCF(vcf, mat78, mat136, mat144 = NULL, sample.id)

Value

The original vcf with three additional columns

DBS78.class, DBS136.class and DBS144.class added.

Arguments

vcf

An in-memory VCF file annotated with sequence context and transcript information by function AnnotateDBSVCF. It must *not* contain indels and must *not* contain SBS (single base substitutions), or triplet base substitutions etc.

mat78

The DBS78 mutation count matrix.

mat136

The DBS136 mutation count matrix.

mat144

The DBS144 mutation count matrix.

sample.id

Usually the sample id, but defaults to "count".