# Generated by roxygen2: do not edit by hand

S3method(print,GbsrGenotypeData)
export("validMar<-")
export("validSam<-")
export(addScheme)
export(assignScheme)
export(boxplotGBSR)
export(closeGDS)
export(countGenotype)
export(countRead)
export(estGeno)
export(gbsrGDS2CSV)
export(gbsrGDS2VCF)
export(gbsrVCF2GDS)
export(getAllele)
export(getChromosome)
export(getCountAlleleAlt)
export(getCountAlleleMissing)
export(getCountAlleleRef)
export(getCountGenoAlt)
export(getCountGenoHet)
export(getCountGenoMissing)
export(getCountGenoRef)
export(getCountRead)
export(getCountReadAlt)
export(getCountReadRef)
export(getFixedParameter)
export(getGenotype)
export(getHaplotype)
export(getInfo)
export(getMAC)
export(getMAF)
export(getMarID)
export(getMeanReadAlt)
export(getMeanReadRef)
export(getMedianReadAlt)
export(getMedianReadRef)
export(getParents)
export(getPloidy)
export(getPosition)
export(getRead)
export(getReplicates)
export(getSDReadAlt)
export(getSDReadRef)
export(getSamID)
export(histGBSR)
export(initScheme)
export(isOpenGDS)
export(loadGDS)
export(makeScheme)
export(nmar)
export(nsam)
export(pairsGBSR)
export(plotDosage)
export(plotGBSR)
export(plotReadRatio)
export(reopenGDS)
export(resetCallFilter)
export(resetFilter)
export(resetMarFilter)
export(resetSamFilter)
export(setCallFilter)
export(setFixedParameter)
export(setInfoFilter)
export(setMarFilter)
export(setParents)
export(setPloidy)
export(setReplicates)
export(setSamFilter)
export(showScheme)
export(thinMarker)
export(validMar)
export(validSam)
exportClasses(GbsrGenotypeData)
exportClasses(GbsrScheme)
importClassesFrom(SeqArray,SeqVarGDSClass)
importFrom(Rcpp,sourceCpp)
importFrom(RcppParallel,defaultNumThreads)
importFrom(RcppParallel,setThreadOptions)
importFrom(SeqArray,seqAddValue)
importFrom(SeqArray,seqApply)
importFrom(SeqArray,seqClose)
importFrom(SeqArray,seqDelete)
importFrom(SeqArray,seqExport)
importFrom(SeqArray,seqGDS2VCF)
importFrom(SeqArray,seqGetData)
importFrom(SeqArray,seqNumAllele)
importFrom(SeqArray,seqOpen)
importFrom(SeqArray,seqOptimize)
importFrom(SeqArray,seqSNP2GDS)
importFrom(SeqArray,seqSetFilter)
importFrom(SeqArray,seqStorageOption)
importFrom(SeqArray,seqSummary)
importFrom(SeqArray,seqVCF2GDS)
importFrom(expm,expm)
importFrom(gdsfmt,add.gdsn)
importFrom(gdsfmt,addfolder.gdsn)
importFrom(gdsfmt,append.gdsn)
importFrom(gdsfmt,apply.gdsn)
importFrom(gdsfmt,closefn.gds)
importFrom(gdsfmt,compression.gdsn)
importFrom(gdsfmt,copyto.gdsn)
importFrom(gdsfmt,createfn.gds)
importFrom(gdsfmt,delete.gdsn)
importFrom(gdsfmt,diagnosis.gds)
importFrom(gdsfmt,exist.gdsn)
importFrom(gdsfmt,index.gdsn)
importFrom(gdsfmt,ls.gdsn)
importFrom(gdsfmt,moveto.gdsn)
importFrom(gdsfmt,objdesp.gdsn)
importFrom(gdsfmt,put.attr.gdsn)
importFrom(gdsfmt,read.gdsn)
importFrom(gdsfmt,readex.gdsn)
importFrom(gdsfmt,readmode.gdsn)
importFrom(gdsfmt,setdim.gdsn)
importFrom(gdsfmt,write.gdsn)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,rel)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linewidth_manual)
importFrom(ggplot2,scale_size_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,stat_smooth)
importFrom(ggplot2,theme)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(methods,"slot<-")
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(stats,cor)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(tidyr,pivot_longer)
importFrom(utils,combn)
importFrom(utils,tail)
importFrom(utils,write.table)
useDynLib(GBScleanR, .registration = TRUE)
