prepareCNMatGistic: Prepare integer valued copy number matrix from Gistic based...

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

Prepare integer valued copy number matrix from Gistic based copy number

Description

The function takes in Gistic values of copy number as obtained from CCLE/TCGA, cell lines of interest and top drivers and returns an integer valued copy number matrix (0 = Homozygous deletion; 1 = Heterozygous deletion; 2 = Normal; etc.).

Usage

prepareCNMatGistic(CN_df_gistic, samples, driver_genes, x)

Arguments

CN_df_gistic	Copy number in Gistic format
samples	vector of cell lines of interest
driver_genes	vector of driver or mutated genes of interest
x	primary site. If 'NULL' then ensure that the 'samples' passed match the colnames of data

Value

Integer valued copy number matrix for selected cell lines and drivers

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