mutsig.gene: Canonical algorithms to detect significantly mutated genes

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

Description

Multiple traditional methods to identify significantly mutated genes based on outputs (*.categs.txt, *.coverage.txt, *.mutations.txt) produced by MutSigCV.

Usage

mutsig.gene(categs.file, coverage.file, mutations.file, mut.df=NULL, output.file, sep="", method=c("PCT","FCPT","LRT","perm.score","perm.num"), exclude.noncoding=FALSE, N=10000, trace=0, only.CGC=FALSE, GOI=NULL, mutations.file.formatted_as_csv=FALSE)

Arguments

categs.file	File with categories mutation rate from MutSigCV, often ended with .categs.txt.
coverage.file	Coverage file from MutSigCV, often ended with .coverage.txt.
mutations.file	Mutation file from MutSigCV, often ended with .mutations.txt.
mut.df	A data frame of mutations.file. mutations.file is ignored if mut.df set.
sep	sep= for mutations.file, set to \t when multiple blank columns present.
output.file	Output file.
method	Method used to identify SMG.
exclude.noncoding	If TRUR, exclude noncoding mutations.
N	Permutation times used in perm.score or perm.num.
trace	If TRUE, print tracing message.
only.CGC	If TRUE, only considers cancer gene census.
GOI	A vector of gene-of-interest(GOI), if provided, only.CGC is set to FALSE.
mutations.file.formatted_as_csv	Formatted mutations.file in csv.

Details

The poisson convolution test (PCT) proposed by Kan et al. in Diverse somatic mutation patterns and pathway alterations in human cancers. The Fisher's combined P-value test (FCPT) and likelihood ratio test (LRT) were 2 of the 3 tests proposed in MuSiC. The perm.score is a permutation procedure used to compute p-value for statistic Sg proposed in page 16 of supplementary of MutSigCV. The perm.num permutes mutation number, instead of Sg, to compute p-value.

PCT, FCPT and perm.score are recommended to use.

Examples

categs.file = "TCGA.Breast_Cancer.MutSigCV.categs.txt"
coverage.file = "TCGA.Breast_Cancer.MutSigCV.coverage.txt"
mutations.file = "TCGA.Breast_Cancer.MutSigCV.mutations.txt"
mutsig.gene(categs.file, coverage.file, mutations.file, sep="\t", output.file="out.PCT")

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