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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method("[",InfDiv)
S3method("[",RangedGlmDataSet)
S3method("[",glmDataSet)
S3method("[",pDMP)
S3method(getDIMPatGenes,GRanges)
S3method(getDIMPatGenes,InfDiv)
S3method(getDIMPatGenes,default)
S3method(getDIMPatGenes,list)
S3method(getDIMPatGenes,pDMP)
S3method(lapply,default)
S3method(predict,LogisticR)
S3method(predict,pcaLDA)
S3method(predict,pcaLogisticR)
S3method(predict,pcaQDA)
S3method(predict,qdaDMP)
S3method(print,CutPoint)
S3method(print,RangedGlmDataSet)
S3method(print,glmDataSet)
S3method(unlist,default)
S3method(validateClass,InfDiv)
S3method(validateClass,default)
S3method(validateClass,pDMP)
export(AICmodel)
export(BICmodel)
export(FisherTest)
export(countTest2)
export(dggamma)
export(dmpClusters)
export(estimateBayesianDivergence)
export(estimateCutPoint)
export(estimateDivergence)
export(estimateECDF)
export(estimateHellingerDiv)
export(estimateJDiv)
export(evaluateDIMPclass)
export(filterByCoverage)
export(filterGRange)
export(fitGGammaDist)
export(fitGammaDist)
export(fitLogNormDist)
export(getDIMPatGenes)
export(getGEOSuppFiles)
export(getPotentialDIMP)
export(glmDataSet)
export(gofReport)
export(lapply)
export(nonlinearFitDist)
export(pcaLDA)
export(pcaLogisticR)
export(pcaQDA)
export(pggamma)
export(poolFromGRlist)
export(predictDIMPclass)
export(pweibull3P)
export(qggamma)
export(readCounts2GRangesList)
export(rggamma)
export(selectDIMP)
export(sortBySeqnameAndStart)
export(uniqueGRanges)
export(uniqueGRfilterByCov)
export(unlist)
export(validateClass)
export(weibull3P)
exportMethods(getDIMPatGenes.GRanges)
exportMethods(predict.ldaDMP)
exportMethods(print.ldaDMP)
exportMethods(print.qdaDMP)
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,unique)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,mcols)
importFrom(IRanges,IRanges)
importFrom(IRanges,reduce)
importFrom(IRanges,width)
importFrom(MASS,glm.nb)
importFrom(MASS,lda)
importFrom(MASS,negative.binomial)
importFrom(MASS,qda)
importFrom(RCurl,getURL)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,extractROWS)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(XML,free)
importFrom(XML,htmlParse)
importFrom(XML,xpathSApply)
importFrom(caret,confusionMatrix)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(genefilter,rowVars)
importFrom(graphics,hist)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowMins)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,show)
importFrom(minpack.lm,nls.lm)
importFrom(minpack.lm,nls.lm.control)
importFrom(minpack.lm,nlsLM)
importFrom(nls2,nls2)
importFrom(rtracklayer,import)
importFrom(stats,AIC)
importFrom(stats,BIC)
importFrom(stats,addmargins)
importFrom(stats,anova)
importFrom(stats,approxfun)
importFrom(stats,as.formula)
importFrom(stats,binom.test)
importFrom(stats,binomial)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,deviance)
importFrom(stats,dpois)
importFrom(stats,ecdf)
importFrom(stats,fisher.test)
importFrom(stats,glm)
importFrom(stats,glm.control)
importFrom(stats,knots)
importFrom(stats,mcnemar.test)
importFrom(stats,na.omit)
importFrom(stats,nlm)
importFrom(stats,nls.control)
importFrom(stats,optim)
importFrom(stats,p.adjust)
importFrom(stats,p.adjust.methods)
importFrom(stats,pbeta)
importFrom(stats,pgamma)
importFrom(stats,plnorm)
importFrom(stats,poisson)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,predict.glm)
importFrom(stats,pweibull)
importFrom(stats,qgamma)
importFrom(stats,quantile)
importFrom(stats,quasipoisson)
importFrom(stats,relevel)
importFrom(stats,resid)
importFrom(stats,rgamma)
importFrom(stats,sd)
importFrom(stats,stepfun)
importFrom(stats,terms)
importFrom(stats,var)
importFrom(stats,vcov)
importFrom(utils,download.file)
importFrom(utils,head)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)