CompositeDriver combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
User will need to install devtools in R for running CompositeDriver package
install.packages("devtools")
library("devtools")
devtools::install_github("khuranalab/CompositeDriver")
User will need to
library(CompositeDriver)
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# global parameters setup
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dataContextDir<-"/path/to/dataContext"
annotatedInput<-"/path/to/Output.vcf"
outputDir<-"/path/to/output"
tumorType<-"GBM"
seedNum<-42
functionalImpactScoreCDS<-"FunSeq2"
functionalImpactScoreNonCoding<-"FunSeq2"
reSampleIter<-1000
useCores<-6
debugMode<-FALSE
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preProcessVCF(annotatedInput,functionalImpactScoreCDS,functionalImpactScoreNonCoding,outputDir,tumorType,useCores)
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mutationType<-"CDS"
cdsOutputDf<-getCDSpvalue(outputDir,tumorType,mutationType,
reSampleIter=reSampleIter,
seedNum=seedNum,debugMode=debugMode)
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For any questions, comments and suggestions, please email
Copyright © 2016-2019 Ekta Khurana Lab, WCMC
This project is licensed under the CC BY-NC 4.0
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