# Generated by roxygen2: do not edit by hand

S3method(plot,GRanges)
S3method(plot,GRangesList)
S3method(plot,aneuBiHMM)
S3method(plot,aneuHMM)
S3method(plot,character)
S3method(print,aneuBiHMM)
S3method(print,aneuHMM)
export(Aneufinder)
export(bam2GRanges)
export(bed2GRanges)
export(binReads)
export(blacklist)
export(breakpointColors)
export(clusterByQuality)
export(clusterHMMs)
export(collapseBins)
export(compareMethods)
export(consensusSegments)
export(correctGC)
export(exportCNVs)
export(exportGRanges)
export(exportReadCounts)
export(filterSegments)
export(findCNVs)
export(findCNVs.strandseq)
export(findHotspots)
export(fixedWidthBins)
export(getBreakpoints)
export(getQC)
export(getSCEcoordinates)
export(heatmapAneuploidies)
export(heatmapGenomewide)
export(heatmapGenomewideClusters)
export(importBed)
export(karyotypeMeasures)
export(loadFromFiles)
export(plotHeterogeneity)
export(plot_pca)
export(refineBreakpoints)
export(simulateReads)
export(stateColors)
export(strandColors)
export(subsetByCNVprofile)
export(variableWidthBins)
import(AneuFinderData)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(doParallel)
import(foreach)
import(ggplot2)
import(reshape2)
importFrom(BiocGenerics,"%in%")
importFrom(Biostrings,BString)
importFrom(Biostrings,BStringSet)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,Views)
importFrom(Biostrings,alphabetFrequency)
importFrom(DNAcopy,CNA)
importFrom(DNAcopy,smooth.CNA)
importFrom(GenomicAlignments,first)
importFrom(GenomicAlignments,granges)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(ReorderCluster,RearrangeJoseph)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,queryHits)
importFrom(bamsignals,bamCount)
importFrom(cowplot,draw_label)
importFrom(cowplot,plot_grid)
importFrom(ecp,e.divisive)
importFrom(ggdendro,dendro_data)
importFrom(ggdendro,theme_dendro)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb2hsv)
importFrom(graphics,plot)
importFrom(mclust,Mclust)
importFrom(mclust,emControl)
importFrom(mclust,mclustBIC)
importFrom(methods,as)
importFrom(methods,is)
importFrom(reshape2,melt)
importFrom(stats,aggregate)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,coefficients)
importFrom(stats,cov.wt)
importFrom(stats,dbinom)
importFrom(stats,dgeom)
importFrom(stats,dist)
importFrom(stats,dnbinom)
importFrom(stats,dnorm)
importFrom(stats,dpois)
importFrom(stats,ecdf)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,na.omit)
importFrom(stats,nls)
importFrom(stats,p.adjust)
importFrom(stats,pbinom)
importFrom(stats,pgeom)
importFrom(stats,pnbinom)
importFrom(stats,predict)
importFrom(stats,qnorm)
importFrom(stats,reshape)
importFrom(stats,rnbinom)
importFrom(stats,runif)
importFrom(stats,stepfun)
importFrom(stats,weighted.mean)
importFrom(utils,head)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.table)
useDynLib(AneuFinder, .registration = TRUE, .fixes = "")
