# 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(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(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,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,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 = "")