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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(addBaf)
export(addCopy)
export(addCoverage)
export(addFakeLogRatio)
export(addGcLogRatio)
export(addGene)
export(addIcaLogRatio)
export(addJointSegment)
export(addLogRatio)
export(addPairLogRatio)
export(addPcaLogRatio)
export(addScaleLogRatio)
export(addSegment)
export(addSmoothLogRatio)
export(analyze)
export(createPool)
export(getOpts)
export(importCNVEX)
export(load)
export(plot)
export(pool)
export(resolveConfig)
export(tocsv)
importFrom(BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,letterFrequency)
importFrom(DNAcopy,CNA)
importFrom(DNAcopy,smooth.CNA)
importFrom(DelayedArray,rowRanges)
importFrom(GenomeInfoDb,"seqinfo<-")
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,"seqnames<-")
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,dropSeqlevels)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,"end<-")
importFrom(GenomicRanges,"mcols<-")
importFrom(GenomicRanges,"start<-")
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,gaps)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,pintersect)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,split)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,width)
importFrom(IRanges,"%over%")
importFrom(MASS,ginv)
importFrom(Rsamtools,BamFile)
importFrom(S4Vectors,"%in%")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(VariantAnnotation,"geno<-")
importFrom(VariantAnnotation,"header<-")
importFrom(VariantAnnotation,"info<-")
importFrom(VariantAnnotation,"qual<-")
importFrom(VariantAnnotation,"vcfWhich<-")
importFrom(VariantAnnotation,ScanVcfParam)
importFrom(VariantAnnotation,fixed)
importFrom(VariantAnnotation,geno)
importFrom(VariantAnnotation,header)
importFrom(VariantAnnotation,info)
importFrom(VariantAnnotation,qual)
importFrom(VariantAnnotation,readVcf)
importFrom(VariantAnnotation,vcfWhich)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,copy)
importFrom(data.table,data.table)
importFrom(data.table,dcast.data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,melt)
importFrom(data.table,rbindlist)
importFrom(data.table,setDT)
importFrom(data.table,setkey)
importFrom(fastICA,fastICA)
importFrom(jointseg,estimateSd)
importFrom(jointseg,jointSeg)
importFrom(limma,loessFit)
importFrom(matrixStats,colMedians)
importFrom(matrixStats,rowMads)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowMins)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(raster,Which)
importFrom(raster,focal)
importFrom(raster,raster)
importFrom(robfilter,hybrid.filter)
importFrom(rtracklayer,export)
importFrom(rtracklayer,import)
importFrom(stringr,str_match)
importFrom(stringr,str_replace)
importFrom(stringr,str_split)
importFrom(stringr,str_sub)