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.

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

`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.

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.

catSBS192 only contains mutations in transcribed regions.

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