getMutMatrix

This function gets the allele frequency for a specific allele. It is used in computeAFMutMatrix. Source: https://github.com/petervangalen/MAESTER-2021

Usage

getMutMatrix(SE, cov, letter, ref_allele, chromosome_prefix)

Arguments

SE

SummarizedExperiment object.

cov

The coverage matrix from MAEGATK/MGATK.

letter

The base we are interested in.

ref_allele

Vector of reference alleles.

chromosome_prefix

The chromosome prefix used.