CreateOneColDBSMatrix: Create the matrix a DBS catalog for *one* sample from an...

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

Description

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

Usage

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

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

Value

A list of three 1-column matrices with the names catDBS78, catDBS136, and catDBS144. If trans.ranges is NULL, catDBS144 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 DBS variants whose tetranucleotide context contains "N", they will be excluded in the analysis and an additional element discarded.variants will appear in the return list.

Note

DBS 144 catalog only contains mutations in transcribed regions.

ICAMS documentation built on April 3, 2021, 5:07 p.m.