CreateOnePPMFromSBSVCF: Create position probability matrix (PPM) for *one* sample...

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

Create position probability matrix (PPM) for *one* sample from a Variant Call Format (VCF) file.

Description

Create position probability matrix (PPM) for *one* sample from a Variant Call Format (VCF) file.

Usage

CreateOnePPMFromSBSVCF(vcf, ref.genome, seq.context.width)

Arguments

vcf	One in-memory data frame of pure SBS mutations – no DBS or 3+BS mutations.
ref.genome	A ref.genome argument as described in ICAMS.
seq.context.width	The number of preceding and following bases to be extracted around the mutated position from ref.genome.

Value

A position probability matrix (PPM).

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