format_counts: Coerce mutation spectra matrix output from Helmsman into...

In carjed/musigtools: musigtools

Description

Coerce mutation spectra matrix output from Helmsman into formats compatible with existing mutation signature analysis packages

Usage

format_counts(M, package)

Arguments

M	Nx96 mutation count matrix output from Helmsman. Each row is a sample ID, and each column is a trinucleotide mutation subtype. Each entry is the count of how many times a mutation with that trinucleotide context is seen in the sample.
package	Name of mutation signature analysis package

Value

A Nx96 data frame with column and row names formatted according to the specifications used Note that the SomaticSignatures packages uses a transposed mutation spectra matrix, with subtypes as row names and sample IDs as column names

Examples

## Not run: 
mu_counts <- read.table("/path/to/subtype_count_matrix.txt", header=T, stringsAsFactors=F)
msm_deconstructSigs <- format_counts(mu_counts, "deconstructSigs")
msm_SomaticSignatures <- format_counts(mu_counts, "SomaticSignatures")
msm_signeR <- format_counts(mu_counts, "signeR")
msm_maftools <- format_counts(mu_counts, "maftools")
msm_MutationalPatterns <- format_counts(mu_counts, "MutationalPatterns")

## End(Not run)

carjed/musigtools documentation built on May 12, 2019, 10:32 p.m.