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

License: MIT License

R 99.93% Shell 0.07%

cncdriver's Introduction

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

License

This project is licensed under the

cncdriver's People

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evanbiederstedt xflicsu inambioinfo duoduoo nalomran

cncdriver's Issues

Usage Section Doesn't Correspond to Actual Function Parameters

For example, preProcessVCF has functionalImpactScoreCDS but when I open the help document using preProcessVCF I see the second parameter is completely different: outputDir Other parameters also don't match up to those shown in Usage. The documentation could also be more informative. For example, all that the Description section states is

Parse Funseq2 VCF file

Perhaps you could use

\references{
  FunSeq2: A Framework for Prioritizing Noncoding Regulatory Variants in Cancer, Yao Fu, Zhu Liu, etc.
}

in the R Documentation file.

Funseq2 output vcf parsing errors

Hi there, first of all thanks for sharing the code and I'm looking forward to your paper when it comes out. This is not an issue of your tool, but I would really appreciate your insight since you have been working with Funseq2 for so long (I guess). I was able to make funseq2.1.6 (downloaded from the official website) work on my data and generate the Output.vcf file, but reading the file with VariantAnnotation::scanVcf (invoked by VariantAnnotation::readVcf) gives me Error: scanVcf: invalid split pattern ',(?=(ID|Number|Type)=[[:alnum:]])|,(?=Description=".?")'. I googled but could not find any solution expect for this thread. I'm wondering if you ever encountered the same problem or if there is any way to bypass the issue and still make your tool work. Thank you for your time!

Below is the first several lines of my Output.vcf file:

##fileformat=VCFv4.0
##INFO=<ID=OTHER,Number=.,Type=String, Description = "Other Information From Original File">
##INFO=<ID=SAMPLE,Number=.,Type=String,Description="Sample id">
##INFO=<ID=CDS,Number=.,Type=String,Description="Coding Variants or not">
##INFO=<ID=VA,Number=.,Type=String,Description="Coding Variant Annotation">
##INFO=<ID=HUB,Number=.,Type=String,Description="Network Hubs, PPI (protein protein interaction network), REG (regulatory network), PHOS (phosphorylation network)...">
##INFO=<ID=GNEG,Number=.,Type=String,Description="Gene Under Negative Selection">
##INFO=<ID=GERP,Number=.,Type=String,Description="Gerp Score">
##INFO=<ID=NCENC,Number=.,Type=String,Description="NonCoding ENCODE Annotation">
##INFO=<ID=HOT,Number=.,Type=String,Description="Highly Occupied Target Region">
##INFO=<ID=MOTIFBR,Number=.,Type=String,Description="Motif Breaking">
##INFO=<ID=MOTIFG,Number=.,Type=String,Description="Motif Gain">
##INFO=<ID=SEN,Number=.,Type=String,Description="In Sensitive Region">
##INFO=<ID=USEN,Number=.,Type=String,Description="In Ultra-Sensitive Region">
##INFO=<ID=UCONS,Number=.,Type=String,Description="In Ultra-Conserved Region">
##INFO=<ID=GENE,Number=.,Type=String,Description="Target Gene (For coding - directly affected genes ; For non-coding - promoter, enhancer regulatory module)">
##INFO=<ID=CANG,Number=.,Type=String,Description="Prior Gene Information, e.g.[cancer][TF_regulating_known_cancer_gene][up_regulated][actionable]...";
##INFO=<ID=CDSS,Number=.,Type=String,Description="Coding Score">
##INFO=<ID=NCDS,Number=.,Type=String,Description="NonCoding Score">
##INFO=<ID=RECUR,Number=.,Type=String,Description="Recurrent elements / variants">
##INFO=<ID=DBRECUR,Number=.,Type=String,Description="Recurrence database">
#CHROM POS ID REF ALT QUAL FILTER INFO
chr13 100252870 . T A . . SAMPLE=T100;GERP=-4.14;CDS=No;HUB=CLYBL:PPI(0.361),TM9SF2:PPI(0.236)REG(0.409);NCENC=DHS(MCV-7|chr13:100252825-100252975),Enhancer(Roadmap_stringent|chr13:100252624-100252923),Enhancer(chmm/segway|chr13:100252783-100253000),TFM(CTCF_DHS|SP1_disc3|chr13:100252864-100252879),TFP(CTCF|chr13:100252207-100252907),TFP(CTCF|chr13:100252476-100252894),TFP(CTCF|chr13:100252487-100252873),TFP(CTCF|chr13:100252497-100252927),TFP(CTCF|chr13:100252503-100252891),TFP(CTCF|chr13:100252503-100252930),TFP(CTCF|chr13:100252505-100252888),TFP(CTCF|chr13:100252514-100253036),TFP(CTCF|chr13:100252515-100252912),TFP(CTCF|chr13:100252515-100252924),TFP(CTCF|chr13:100252516-100252910),TFP(CTCF|chr13:100252517-100252885),TFP(CTCF|chr13:100252519-100252971),TFP(CTCF|chr13:100252524-100252882),TFP(CTCF|chr13:100252527-100252884),TFP(CTCF|chr13:100252531-100252949),TFP(CTCF|chr13:100252532-100252884),TFP(CTCF|chr13:100252533-100252888),TFP(CTCF|chr13:100252535-100252892),TFP(CTCF|chr13:100252539-100252884),TFP(CTCF|chr13:100252541-100252876),TFP(CTCF|chr13:100252548-100252894),TFP(CTCF|chr13:100252564-100252892),TFP(CTCF|chr13:100252575-100252873),TFP(CTCF|chr13:100252587-100252877),TFP(CTCF|chr13:100252589-100252892),TFP(RAD21|chr13:100252520-100252938),TFP(RAD21|chr13:100252524-100252936),TFP(RAD21|chr13:100252529-100252933),TFP(RAD21|chr13:100252531-100252912),TFP(RAD21|chr13:100252537-100252892),TFP(RAD21|chr13:100252537-100252897);HOT=H1hesc;MOTIFBR=CTCF_DHS#SP1_disc3#100252864#100252879#-#10#0.131148#0.245902;MOTIFG=MZF1_3#100252864#100252870#-#1#6.892#5.961;SEN=Yes;GENE=CLYBL(Distal)TM9SF2(Distal);NCDS=3.854994663534:4.854994663534;RECUR=TFP(CTCF|chr13:100252207-100252907):T100&T236,TFP(CTCF|chr13:100252476-100252894):T100&T236
chr4 60720 . T C . . SAMPLE=T100;GERP=0.69;CDS=No;HUB=ZNF595:REG(0.987);NCENC=TFM(MAFF_MAFK|CEBPG_1|chr4:60714-60727),TFP(CHD2|chr4:50497-61009),TFP(EP300|chr4:57632-61054),TFP(FAM48A|chr4:58427-60880),TFP(FAM48A|chr4:59515-61055),TFP(FOS|chr4:55158-60924),TFP(IRF3|chr4:60169-61169),TFP(JUND|chr4:50500-62894),TFP(KAT2A|chr4:59928-60898),TFP(MAFF|chr4:60004-61056),TFP(MAFK|chr4:50489-63382),TFP(MAFK|chr4:59870-61092),TFP(MAFK|chr4:60116-61036),TFP(MXI1|chr4:50616-61014),TFP(SIN3A|chr4:52691-62808),TFP(STAT1|chr4:60005-61046),TFP(ZZZ3|chr4:59671-60953);HOT=K562;MOTIFBR=MAFF_MAFK#CEBPG_1#60714#60727#+#6#0.000000#0.714286;SEN=Yes;USEN=Yes;GENE=ZNF595(Intron);NCDS=3.7416745628426:4.7416745628426;RECUR=TFP(CHD2|chr4:50497-61009):T100&T104&T106&T107&T11&T115&T153&T157&T167&T252&T256&T258&T264&T267&T272&T275&T284&T294&T297&T300&T314&T318&T59&T70&T80&T92,TFP(EP300|chr4:57632-61054):T100&T104&T106&T107&T264&T272&T275&T333&T59&T80&T92,TFP(FAM48A|chr4:58427-60880):T100&T264&T272&T59&T80&T92,TFP(FAM48A|chr4:59515-61055):T100&T106&T264&T272&T333&T59&T80,TFP(FOS|chr4:55158-60924):T100&T104&T106&T107&T115&T256&T264&T272&T275&T294&T297&T318&T59&T80&T92,TFP(IRF3|chr4:60169-61169):T100&T106&T264&T272&T333&T80,TFP(JUND|chr4:50500-62894):T100&T104&T106&T107&T108&T11&T115&T153&T157&T167&T252&T256&T258&T264&T267&T272&T275&T284&T294&T297&T300&T314&T318&T333&T52&T59&T70&T80&T92,TFP(KAT2A|chr4:59928-60898):T100&T264&T272&T80,TFP(MAFF|chr4:60004-61056):T100&T106&T264&T272&T333&T80,TFP(MAFK|chr4:50489-63382):T100&T104&T106&T107&T108&T11&T115&T153&T157&T167&T252&T256&T258&T264&T267&T272&T275&T284&T294&T297&T300&T314&T318&T333&T52&T59&T70&T80&T92,TFP(MAFK|chr4:59870-61092):T100&T106&T264&T272&T333&T80,TFP(MAFK|chr4:60116-61036):T100&T106&T264&T272&T80,TFP(MXI1|chr4:50616-61014):T100&T104&T106&T107&T11&T115&T153&T157&T167&T252&T256&T258&T264&T267&T272&T275&T284&T294&T297&T300&T314&T318&T59&T70&T80&T92,TFP(SIN3A|chr4:52691-62808):T100&T104&T106&T107&T108&T11&T115&T153&T252&T256&T258&T264&T272&T275&T284&T294&T297&T314&T318&T333&T59&T80&T92,TFP(STAT1|chr4:60005-61046):T100&T106&T264&T272&T333&T80,TFP(ZZZ3|chr4:59671-60953):T100&T264&T272&T59&T80;DBRECUR=TFP(CHD2|chr4:50497-61009):Lung_Adeno(Altered in 17/24(70.83%) samples.)|Pancreas(Altered in 2/15(13.33%) samples.)|Prostate(Altered in 5/64(7.81%) samples.),TFP(EP300|chr4:57632-61054):Lung_Adeno(Altered in 10/24(41.67%) samples.),TFP(FAM48A|chr4:58427-60880):Lung_Adeno(Altered in 7/24(29.17%) samples.),TFP(FAM48A|chr4:59515-61055):Lung_Adeno(Altered in 6/24(25.00%) samples.),TFP(FOS|chr4:55158-60924):Lung_Adeno(Altered in 14/24(58.33%) samples.)|Prostate(Altered in 2/64(3.12%) samples.),TFP(JUND|chr4:50500-62894):Lung_Adeno(Altered in 17/24(70.83%) samples.)|Pancreas(Altered in 2/15(13.33%) samples.)|Prostate(Altered in 5/64(7.81%) samples.),TFP(KAT2A|chr4:59928-60898):Lung_Adeno(Altered in 3/24(12.50%) samples.),TFP(MAFF|chr4:60004-61056):Lung_Adeno(Altered in 3/24(12.50%) samples.),TFP(MAFK|chr4:50489-63382):Lung_Adeno(Altered in 17/24(70.83%) samples.)|Pancreas(Altered in 2/15(13.33%) samples.)|Prostate(Altered in 5/64(7.81%) samples.),TFP(MAFK|chr4:59870-61092):Lung_Adeno(Altered in 3/24(12.50%) samples.),TFP(MXI1|chr4:50616-61014):Lung_Adeno(Altered in 17/24(70.83%) samples.)|Pancreas(Altered in 2/15(13.33%) samples.)|Prostate(Altered in 5/64(7.81%) samples.),TFP(SIN3A|chr4:52691-62808):Lung_Adeno(Altered in 17/24(70.83%) samples.)|Prostate(Altered in 4/64(6.25%) samples.),TFP(STAT1|chr4:60005-61046):Lung_Adeno(Altered in 3/24(12.50%) samples.),TFP(ZZZ3|chr4:59671-60953):Lung_Adeno(Altered in 4/24(16.67%) samples.)

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