# Generated by roxygen2: do not edit by hand

export(annotateTargets)
export(bootstrapResults)
export(calculateBamCoverageByInterval)
export(calculateGCContentByInterval)
export(calculateIntervalWeights)
export(calculateLogRatio)
export(calculateMappingBiasVcf)
export(calculatePowerDetectSomatic)
export(calculateTangentNormal)
export(callAlterations)
export(callAlterationsFromSegmentation)
export(callLOH)
export(callMutationBurden)
export(correctCoverageBias)
export(createCurationFile)
export(createNormalDatabase)
export(createTargetWeights)
export(filterIntervals)
export(filterTargets)
export(filterVcfBasic)
export(filterVcfMuTect)
export(filterVcfMuTect2)
export(findFocal)
export(getSexFromCoverage)
export(getSexFromVcf)
export(plotAbs)
export(poolCoverage)
export(predictSomatic)
export(preprocessIntervals)
export(processMultipleSamples)
export(readCoverageFile)
export(readCurationFile)
export(runAbsoluteCN)
export(segmentationCBS)
export(segmentationHclust)
export(segmentationPSCBS)
export(setMappingBiasVcf)
export(setPriorVcf)
import(DNAcopy)
import(IRanges)
import(VariantAnnotation)
importFrom(BiocGenerics,unstrand)
importFrom(Biostrings,letterFrequency)
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,genomeStyles)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicFeatures,exonsByOverlaps)
importFrom(GenomicFeatures,transcriptsByOverlaps)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,tile)
importFrom(GenomicRanges,tileGenome)
importFrom(Matrix,tcrossprod)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,TabixFile)
importFrom(Rsamtools,headerTabix)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanFa)
importFrom(Rsamtools,scanFaIndex)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,expand)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VGAM,dbetabinom.ab)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(futile.logger,appender.tee)
importFrom(futile.logger,flog.appender)
importFrom(futile.logger,flog.debug)
importFrom(futile.logger,flog.fatal)
importFrom(futile.logger,flog.info)
importFrom(futile.logger,flog.threshold)
importFrom(futile.logger,flog.warn)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_trans)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_alpha_continuous)
importFrom(ggplot2,scale_y_sqrt)
importFrom(ggplot2,stat_density2d)
importFrom(ggplot2,theme)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,boxplot)
importFrom(graphics,contour)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,strwidth)
importFrom(graphics,symbols)
importFrom(graphics,text)
importFrom(gridExtra,grid.arrange)
importFrom(methods,is)
importFrom(rhdf5,H5Fopen)
importFrom(rtracklayer,import)
importFrom(stats,C)
importFrom(stats,aggregate)
importFrom(stats,binom.test)
importFrom(stats,complete.cases)
importFrom(stats,cutree)
importFrom(stats,dbeta)
importFrom(stats,dbinom)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,dunif)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,pbeta)
importFrom(stats,predict)
importFrom(stats,runif)
importFrom(stats,t.test)
importFrom(stats,weighted.mean)
importFrom(tools,file_ext)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,object.size)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(utils,write.table)