Description Usage Arguments Details Examples
View source: R/mutsigcv.sig.pathway.R
Identify significantly mutated pathways (SMP) through combining p-values that computed for each gene, e.g. output produced by MutSigCV.
1 | mutsigcv.sig.pathway(mutsigcv.sig_gene.filename, pathway, out.filename=NA, exclude.genes=c(), min.n_nonsilent=0)
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mutsigcv.sig_gene.filename |
Output file generated by MutSigCV, often ended with |
pathway |
A data frame with 3 cols containg pathway information, see |
out.filename |
output file. |
exclude.genes |
Genes to be excluded. |
min.n_nonsilent |
min number of nonsilent mutations required. |
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
1 2 3 4 5 | 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)
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