CNCDriver

References

Eric Minwei Liu, Alexander Martinez Fundichely, Bianca Jay Diaz, Boaz Aronson, Tawny Cuykendall, Matthew MacKay, Priyanka Dhingra, Elissa WP Wong, Ping Chi, Effie Apostolou, Neville E Sanjana, Ekta Khurana “Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes”, Cell Systems, 8,4460455. e8 (2019)

Overview

CNCDriver combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers

Version notes

CNCDriver (version 0.3.3) add tutorial, Oct-10-2019
CNCDriver (version 0.3.2) bugs fix
CNCDriver (version 0.3.1) variable refacoring
CNCDriver (version 0.3) supports SNV coding drivers, promoter, enhancer, lincRNA and CTCF/cohesin insulator

Installation

User will need to install devtools in R for running CNCDriver package

library("remotes")
remotes::install_github("khuranalab/CNCDriver", ref="master", build_vignette=TRUE)

Usage

library(CNCDriver)

#####
# global parameters setup
#####

  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

#####
  
  preProcessVCF(annotatedInput,functionalImpactScoreCDS,functionalImpactScoreNonCoding,outputDir,tumorType,useCores)

#####

  mutationType<-"promoter"
  elementKeyWord<-"Promoter"
  
  promoterOutputDf<-getPromoterPvalue(inputFileDir,outputFileDir,
                                      promoterRegionBedFile,elementKeyWord,
                                      triNucleotideDistributionFile,
                                      filterOutBlacklistMutations,mutationBlacklistFile,
                                      replicationTimingGenomeBinnedFile,replicationTimingElementBinnedFilePromoter,
                                      tumorType,mutationType,cellType,replicationTimingCutOff,
                                      seedNum,reSampleIterations,reRunPvalueCutOff,
                                      useCores,taskNum,unitSize,debugMode)




#####

  mutationType<-"lincRNA"
  elementKeyWord<-"lincRNA"
  
  lincRNAOutputDf<-getLincRNAPvalue(inputFileDir,outputFileDir,
                                    lincRNARegionBedFile,elementKeyWord,
                                    triNucleotideDistributionFile,
                                    filterOutBlacklistMutations,mutationBlacklistFile,
                                    replicationTimingGenomeBinnedFile,replicationTimingElementBinnedFileLincRNA,
                                    tumorType,mutationType,cellType,replicationTimingCutOff,
                                    seedNum,reSampleIterations,reRunPvalueCutOff,
                                    useCores,taskNum,unitSize,debugMode)


#####


  mutationType<-"enhancerUnit"
  elementKeyWord<-"Distal"
  
  enhancerUnitOutputDf<-getEnhancerUnitPvalue(inputFileDir,outputFileDir,
                                              enhancerRegionBedFile,elementKeyWord,
                                              triNucleotideDistributionFile,
                                              filterOutBlacklistMutations,mutationBlacklistFile,
                                              replicationTimingGenomeBinnedFile,replicationTimingElementBinnedFileEnhancer,
                                              tumorType,mutationType,cellType,replicationTimingCutOff,
                                              seedNum,reSampleIterations,reRunPvalueCutOff,
                                              useCores,taskNum,unitSize,debugMode)

#####

#####

Contacts

For any questions, comments and suggestions, please email

ekk2003 [at] med.cornell.edu
mil2041 [at] med.cornell.edu

License

This project is licensed under the

nalomran/CNCDriver