# Generated by roxygen2: do not edit by hand

export(analyzeSNPhood)
export(annotationBins)
export(annotationBins2)
export(annotationDatasets)
export(annotationReadGroups)
export(annotationRegions)
export(associateGenotypes)
export(changeObjectIntegrityChecking)
export(collectFiles)
export(convertToAllelicFractions)
export(deleteDatasets)
export(deleteReadGroups)
export(deleteRegions)
export(enrichment)
export(getDefaultParameterList)
export(mergeReadGroups)
export(nBins)
export(nDatasets)
export(nReadGroups)
export(nRegions)
export(parameters)
export(plotAllelicBiasResults)
export(plotAllelicBiasResultsOverview)
export(plotAndCalculateCorrelationDatasets)
export(plotAndCalculateWeakAndStrongGenotype)
export(plotAndClusterMatrix)
export(plotAndSummarizeAllelicBiasTest)
export(plotBinCounts)
export(plotClusterAverage)
export(plotFDRResults)
export(plotGenotypesPerCluster)
export(plotGenotypesPerSNP)
export(plotRegionCounts)
export(renameBins)
export(renameDatasets)
export(renameReadGroups)
export(renameRegions)
export(results)
export(testForAllelicBiases)
exportMethods(annotation)
exportMethods(counts)
exportMethods(enrichment)
exportMethods(parameters)
import(GenomicRanges)
import(Rsamtools)
import(checkmate)
importFrom(BiocGenerics,annotation)
importFrom(BiocGenerics,counts)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpok)
importFrom(BiocParallel,multicoreWorkers)
importFrom(Biostrings,nucleotideFrequencyAt)
importFrom(Biostrings,subseq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,sizeFactors)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,fetchExtendedChromInfoFromUCSC)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,as.matrix)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,countBam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(S4Vectors,as.table)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VariantAnnotation,ScanVcfParam)
importFrom(VariantAnnotation,alt)
importFrom(VariantAnnotation,geno)
importFrom(VariantAnnotation,readVcf)
importFrom(VariantAnnotation,ref)
importFrom(VariantAnnotation,samples)
importFrom(VariantAnnotation,scanVcfHeader)
importFrom(cluster,clara)
importFrom(cluster,silhouette)
importFrom(cluster,sortSilhouette)
importFrom(data.table,":=")
importFrom(data.table,data.table)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplotGrob)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_discrete)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,gray)
importFrom(grDevices,hsv)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb2hsv)
importFrom(grid,grid.draw)
importFrom(gridExtra,grid.arrange)
importFrom(lattice,levelplot)
importFrom(lattice,panel.abline)
importFrom(lattice,panel.levelplot)
importFrom(methods,new)
importFrom(methods,validObject)
importFrom(reshape2,melt)
importFrom(scales,comma)
importFrom(stats,binom.test)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,median)
importFrom(stats,sd)
importFrom(utils,head)
importFrom(utils,object.size)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,tail)
