vcf2mut_cat: Derive the mutational catalogue from a vcf

In SigsPack: Mutational Signature Estimation for Single Samples

Description

Creates a matrix containing the mutational catalogue from a vcf file or object. The result can be input to the analysis functions of this package.

Usage

vcf2mut_cat(vcf, genome, name = NULL, seqs = NULL)

Arguments

vcf	*.vcf file or a vcf object containing variant calling data for one patient
genome	a BSgenome object corresponding to the genome the variants were called on
name	optional, a sample name
seqs	optional, a character vector containing the names of the sequences that are to be included in the mutational profile. If none is given everything will we included

Value

mutational catalogue (matrix) of a patient containing SNV absolute counts (in the 96 trinucleotide context) format: 1 by 96

Note

The execution can take some time, depending on the size of the vcf

Examples

## Not run: 
vcf2mut_cat('test.vcf', BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)

## End(Not run)

SigsPack documentation built on Nov. 8, 2020, 6:57 p.m.