# Generated by roxygen2: do not edit by hand

export(bootstrapDist)
export(calGeneticDist)
export(combineHapState)
export(correctGT)
export(countBinState)
export(countCOs)
export(countGT)
export(filterGT)
export(findDupSamples)
export(getAFTracks)
export(getCellAFTrack)
export(getCellCORange)
export(getCellDPTrack)
export(getDistortedMarkers)
export(getMeanDPTrack)
export(getSNPDensityTrack)
export(perCellChrQC)
export(perSegChrQC)
export(permuteDist)
export(plotCount)
export(plotGTFreq)
export(plotGeneticDist)
export(plotWholeGenome)
export(readColMM)
export(readHapState)
import(ggplot2)
import(methods)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(BiocParallel,bplapply)
importFrom(GenomeInfoDb,"genome<-")
importFrom(GenomeInfoDb,genome)
importFrom(GenomeInfoDb,getChromInfoFromUCSC)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicRanges,"mcols<-")
importFrom(GenomicRanges,"seqinfo<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,binnedAverage)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,gaps)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,mcolAsRleList)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,sort)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,width)
importFrom(Gviz,DataTrack)
importFrom(IRanges,IRanges)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,mergeByOverlaps)
importFrom(IRanges,ranges)
importFrom(IRanges,start)
importFrom(IRanges,width)
importFrom(Matrix,Matrix)
importFrom(Matrix,readMM)
importFrom(Matrix,rowMeans)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,elementMetadata)
importFrom(S4Vectors,from)
importFrom(S4Vectors,merge)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,to)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"metadata<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(circlize,colorRamp2)
importFrom(dplyr,"%>%")
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,if_else)
importFrom(dplyr,lag)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(grid,gpar)
importFrom(grid,grid.circle)
importFrom(grid,grid.rect)
importFrom(grid,grid.text)
importFrom(gridExtra,grid.arrange)
importFrom(plotly,plot_ly)
importFrom(plotly,subplot)
importFrom(plyr,mapvalues)
importFrom(reshape2,melt)
importFrom(rlang,.data)
importFrom(scales,unit_format)
importFrom(stats,chisq.test)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(tidyr,pivot_longer)
importFrom(utils,read.table)
