README.md

In mil2041/CNCDriver: CNCDriver

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
#####

  funseq2OutFile<-"path/to/funseq2/annotatedfile"

  replicationTimingCutOff<-0.2
  filterOutBlacklistMutations<-TRUE

  seedNum<-42
  reSampleIterations<-10000
  reRunPvalueCutOff<-0.1

  minPoints<-2
  dRadius<-50

  useCores<-4
  debugMode<-FALSE

  taskNum<-0
  unitSize<-100


#####

    mutationType<-"cds_cluster"
    elementKeyWord<-"CDS"

    cdsOutputDf<-getCDSPvalueWithPreFilter2(inputFileDir,outputFileDir,
                                           codingRegionBedFile,elementKeyWord,
                                           proteinDomainFile,proteinLengthFile,
                                           minPoints,dRadius,
                                           triNucleotideDistributionFile,
                                           filterOutBlacklistMutations,
                                           mutationBlacklistFile,
                                           replicationTimingGenomeBinnedFile,
                                           replicationTimingElementBinnedFileCDS,
                                           tumorType,mutationType,cellType,
                                           replicationTimingCutOff,
                                           seedNum,reSampleIterations,
                                           reRunPvalueCutOff,
                                           useCores,taskNum,unitSize,debugMode)

    makeQQplot(cdsOutputDf)

#####

    mutationType<-"promoter_cluster"
    elementKeyWord<-"Promoter"

    promoterOutputDf<-getPromoterPvalueWithPreFilter2(inputFileDir,outputFileDir,
                                        promoterRegionBedFile,elementKeyWord,
                                        minPoints,dRadius,
                                        triNucleotideDistributionFile,
                                        filterOutBlacklistMutations,
                                        mutationBlacklistFile,
                                        replicationTimingGenomeBinnedFile,
                                        replicationTimingElementBinnedFilePromoter,
                                        tumorType,mutationType,cellType,
                                        replicationTimingCutOff,
                                        seedNum,reSampleIterations,
                                        reRunPvalueCutOff,
                                        useCores,taskNum,unitSize,debugMode)

    makeQQplot(promoterOutputDf)


#####

    mutationType<-"lincRNA_cluster"
    elementKeyWord<-"lincRNA"

    lincRNAOutputDf<-getLincRNAPvalueWithPreFilter2(inputFileDir,outputFileDir,
                                      lincRNARegionBedFile,elementKeyWord,
                                      minPoints,dRadius,
                                      triNucleotideDistributionFile,
                                      filterOutBlacklistMutations,
                                      mutationBlacklistFile,
                                      replicationTimingGenomeBinnedFile,
                                      replicationTimingElementBinnedFileLincRNA,
                                      tumorType,mutationType,cellType,
                                      replicationTimingCutOff,
                                      seedNum,reSampleIterations,
                                      reRunPvalueCutOff,
                                      useCores,taskNum,unitSize,debugMode)


    makeQQplot(lincRNAOutputDf)



#####

    mutationType<-"enhancerUnit_cluster"
    elementKeyWord<-"Distal"

    enhancerUnitOutputDf<-getEnhancerUnitPvalueWithPreFilter2(inputFileDir,
                                                            outputFileDir,
                                              enhancerRegionBedFile,
                                              elementKeyWord,
                                              minPoints,dRadius,
                                              triNucleotideDistributionFile,
                                              filterOutBlacklistMutations,
                                              mutationBlacklistFile,
                                              replicationTimingGenomeBinnedFile,
                                              replicationTimingElementBinnedFileEnhancer,
                                              tumorType,mutationType,cellType,
                                              replicationTimingCutOff,
                                              seedNum,reSampleIterations,
                                              reRunPvalueCutOff,
                                              useCores,taskNum,unitSize,
                                              debugMode)


     makeQQplot(enhancerUnitOutputDf)

#####

Contacts

For any questions, comments and suggestions, please email

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

Copyright © 2016-2019 Ekta Khurana Lab, WCMC

License

This project is licensed under the

mil2041/CNCDriver documentation built on Dec. 13, 2020, 3:41 a.m.