mutsigcv.sig.pathway: Identify significantly mutated pathways based on MutSigCV...

In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description

Identify significantly mutated pathways (SMP) through combining p-values that computed for each gene, e.g. output produced by MutSigCV.

Usage

mutsigcv.sig.pathway(mutsigcv.sig_gene.filename, pathway, out.filename=NA, exclude.genes=c(), min.n_nonsilent=0)

Arguments

mutsigcv.sig_gene.filename	Output file generated by MutSigCV, often ended with .sig_genes.txt.
pathway	A data frame with 3 cols containg pathway information, see details for detail.
out.filename	output file.
exclude.genes	Genes to be excluded.
min.n_nonsilent	min number of nonsilent mutations required.

Details

Identification of SMPs based on combining p-values.

pathway, a data frame, with 3 columns, for example:

PathwayID PathwayName Genes
pathway1 RB signaling A,B,C,D,E
pathway2 TP53 signaling C,D,F,G,H

Examples

mutsigcv.sig_gene.filename <- "EC.sig_genes.txt"
pathway.filename <- "/ifshk1/BC_CANCER/03user/lixiangchun/db/pathway/BroadCuratedPathway/classic_cancer_pathway.lxc4"
pathway <- read.table(pathway.filename, sep="\t")
out.filename = "EC.sig_pathways.txt"
mutsigcv.sig.pathway(mutsigcv.sig_gene.filename, pathway, out.filename)

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.