AddAndCheckSBSClassInVCF: Add and check SBS class in an annotated VCF with the...

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

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

Description

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

Usage

AddAndCheckSBSClassInVCF(vcf, mat96, mat1536, mat192 = NULL, sample.id)

Arguments

vcf	An in-memory VCF file annotated with sequence context and transcript information by function AnnotateSBSVCF. It must *not* contain indels and must *not* contain DBS (double base substitutions), or triplet base substitutions etc., even if encoded as neighboring SBS.
mat96	The SBS96 mutation count matrix.
mat1536	The SBS1536 mutation count matrix.
mat192	The SBS192 mutation count matrix.
sample.id	Usually the sample id, but defaults to "count".

Value

The original vcf with three additional columns SBS96.class, SBS192.class and SBS1536.class added.

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