mutsig.pathway: Canonical algorithms to detect significantly mutated genes
In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description Usage Arguments Details Examples

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

1	mutsig.pathway(categs.file, coverage.file, mutations.file, output.file, pathway, sep="", method=c("PCT"), exclude.noncoding=FALSE, only.mutated.gene=FALSE, trace=1, cancer.genes=c())

`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`.
`sep`	`sep=` for mutations.file, set to `\t` when multiple blank columns present.
`output.file`	Output file.
`pathway`	A data frame with 3 cols containg pathway information, the same as the one in `mutsigcv.sig.pathway`; A data frame of pathway is used if not provided.
`method`	Method used to identify SMP, currently only PCT is supported.
`exclude.noncoding`	If TRUR, exclude `noncoding` mutations.
`only.mutated.gene`	If TRUR, exclude `noncoding` mutations in estimating expected mutation number.
`trace`	If TRUE, print tracing message.
`cancer.genes`	If provided, only considers genes that is subset of `cancer.genes`.

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.

categs.file = "TCGA.Breast_Cancer.MutSigCV.categs.txt"
coverage.file = "TCGA.Breast_Cancer.MutSigCV.coverage.txt"
mutations.file = "TCGA.Breast_Cancer.MutSigCV.mutations.txt"
data("CanonicalCancerPathway", package="lxctk")
mutsig.pathway(categs.file, coverage.file, mutations.file, pathway, sep="\t", output.file="out.PCT")