prepareMutMat: Prepare mutation matrix

In cbg-ethz/slidr: Discovery of mutation-specific synthetic lethal partners from large pan-cancer perturbation screens

Prepare mutation matrix

Description

Function takes in a list of driver genes, samples and mutation/maf file and returns a binary muration matrix

Usage

prepareMutMat(x, driver_genes, samples, all_cancers_mut_df)

Arguments

x	primary site. If 'NULL' then ensure that the 'samples' passed match the 'Tumor_Sample_Barcode' field in 'all_cancers_mut_df'
driver_genes	vector of interested driver genes
samples	vector of cell lines or patient samples
all_cancers_mut_df	dataframe of mutations with Hugo_symbol, Tumor_Sample_Barcode and type of mutation

Value

a mutation matrix for the given samples and genes

cbg-ethz/slidr documentation built on Feb. 8, 2023, 11:15 p.m.