EV
evanbiederstedt/FSig-SNV
FSig-SNV: An R package detecting SNV coding and non-coding drivers in cancer
FSig-SNV
An R package detecting SNV coding and non-coding drivers in cancer
Installing FSig-SNV
You will need to install devtools for running FSigSNV package
install.packages("devtools")
library("devtools")
devtools::install_github("khuranalab/FSig-SNV")FSig-SNV example
User will need to
- (1) download drm.gene.bed file and put it in the "/path/to/dataContext" folder
- (2) assign "/path/to/Output.vcf" path for FunSeq2 annotated vcf file
- (3) assign "/path/to/output" path for saving FSig-SNV results
- (4) tumorType: name of tumor type
- (5) useCores: number of cores for parellel computation
- (6) seedNum: random number seed number (default is 42)
- (7) reSampleIter: sampling iterations (suggesting number is 1000000 iterations)
library(FSigSNV)
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# global parameters setup
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dataContextDir<-"/path/to/dataContext"
funseq2OutputFile<-"/path/to/Output.vcf"
outputDir<-"/path/to/output"
tumorType<-"Prostate"
seedNum<-42
reSampleIter<-1000
useCores<-6
debugMode<-FALSE
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preProcessVCF(funseq2OutputFile,outputDir,tumorType,useCores)
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mutationType<-"CDS"
cdsOutputDf<-getCDSpvalue(outputDir,tumorType,mutationType,
reSampleIter=reSampleIter,
seedNum=seedNum,debugMode=debugMode)
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mutationType<-"promoter"
promoterOutputDf<-getPromoterPvalue(outputDir,tumorType,mutationType,
reSampleIter=reSampleIter,
seedNum=seedNum,debugMode=debugMode)
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mutationType<-"lincRNA"
lincRNAOutputDf<-getLincRNAPvalue(outputDir,tumorType,mutationType,
reSampleIter=reSampleIter,
seedNum=seedNum,debugMode=debugMode)
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fileName<-"drm.gene.bed"
fileName<-file.path(dataContextDir,fileName)
enhancerGeneInteractionFileName<-fileName
mutationType<-"enhancerUnit"
enhancerUnitOutputDf<-getEnhancerUnitPvalue(outputDir,tumorType,mutationType,
reSampleIter=reSampleIter,
seedNum=seedNum,
enhancerGeneInteractionFileName,
useCores=useCores,
debugMode=debugMode)
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