# Generated by roxygen2: do not edit by hand

 S3method(print,combinedMultiHMM)
 S3method(print,multiHMM)
 S3method(print,uniHMM)

 export(Chromstar)

 export(bin2dec)

 export(binReads)

 export(callPeaksMultivariate)

 export(callPeaksReplicates)

 export(callPeaksUnivariate)

 export(changeFDR)

 export(changeMaxPostCutoff)

 export(changePostCutoff)

 export(collapseBins)

 export(combineMultivariates)

 export(dec2bin)

 export(exportCombinations)
 export(exportCounts)

 export(exportGRangesAsBedFile)

 export(exportPeaks)

 export(fixedWidthBins)

 export(genomicFrequencies)

 export(getCombinations)

 export(getDistinctColors)

 export(getStateColors)

 export(heatmapCombinations)

 export(heatmapCountCorrelation)

 export(heatmapTransitionProbs)

 export(loadHmmsFromFiles)

 export(plotEnrichCountHeatmap)

 export(plotEnrichment)

 export(plotExpression)

 export(plotFoldEnrichHeatmap)

 export(plotGenomeBrowser)

 export(plotHistogram)

 export(readBamFileAsGRanges)
 export(readBedFileAsGRanges)

 export(readCustomBedFile)

 export(removeCondition)

 export(stateBrewer)

 export(transitionFrequencies)

 export(unis2pseudomulti)

 export(variableWidthBins)

 import(GenomeInfoDb)

 import(GenomicRanges)
 import(IRanges)

 import(chromstaRData)

 import(doParallel)
 import(foreach)

 import(ggplot2)

 importFrom(GenomicAlignments,first)

 importFrom(GenomicAlignments,readGAlignmentPairs)
 importFrom(GenomicAlignments,readGAlignments)

 importFrom(IRanges,subsetByOverlaps)

 importFrom(Rsamtools,BamFile)

 importFrom(Rsamtools,ScanBamParam)
 importFrom(Rsamtools,indexBam)
 importFrom(Rsamtools,scanBamFlag)

 importFrom(S4Vectors,Rle)

 importFrom(S4Vectors,as.factor)

 importFrom(S4Vectors,endoapply)

 importFrom(S4Vectors,queryHits)

 importFrom(S4Vectors,runmean)

 importFrom(S4Vectors,subjectHits)

 importFrom(bamsignals,bamCount)

 importFrom(grDevices,col2rgb)

 importFrom(grDevices,rgb2hsv)

 importFrom(graphics,hist)

 importFrom(methods,as)
 importFrom(methods,is)

 importFrom(mvtnorm,rmvnorm)

 importFrom(reshape2,melt)

 importFrom(stats,aggregate)
 importFrom(stats,cutree)
 importFrom(stats,dist)
 importFrom(stats,dnbinom)
 importFrom(stats,dnorm)

 importFrom(stats,ecdf)

 importFrom(stats,hclust)
 importFrom(stats,pnbinom)
 importFrom(stats,qnorm)
 importFrom(stats,rbinom)
 importFrom(stats,rnbinom)
 importFrom(stats,runif)
 importFrom(stats,stepfun)
 importFrom(utils,read.table)
 importFrom(utils,write.table)
 useDynLib(chromstaR, .registration = TRUE, .fixes = "")