AddAndCheckDBSClassInVCF: Add and check DBS class in an annotated VCF with the...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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)

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".

Value

The original vcf with three additional columns DBS78.class, DBS136.class and DBS144.class added.

ICAMS documentation built on June 22, 2024, 6:47 p.m.