CreateOneColSBSMatrix: Create the matrix an SBS catalog for *one* sample from an...

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

Create the matrix an SBS catalog for *one* sample from an in-memory VCF.

Description

Create the matrix an SBS catalog for *one* sample from an in-memory VCF.

Usage

CreateOneColSBSMatrix(vcf, sample.id = "count", return.annotated.vcf = FALSE)

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.
sample.id	Usually the sample id, but defaults to "count".
return.annotated.vcf	Whether to return the annotated VCF with additional columns showing the mutation class for each variant. Default is FALSE.

Value

A list of three 1-column matrices with the names catSBS96, catSBS192, catSBS1536. If transcript information is not available in vcf, catSBS192 is not generated. Do not rely on the order of elements in the list. If return.annotated.vcf = TRUE, another element annotated.vcf will appear in the list. If there are SBS variants whose pentanucleotide context contains "N", they will be excluded in the analysis and an additional element discarded.variants will appear in the return list.

Note

catSBS192 only contains mutations in transcribed regions.

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