# Generated by roxygen2: do not edit by hand

export(addScan)
export(addScheme)
export(boxplotGBSR)
export(calcReadStats)
export(closeGDS)
export(countGenotype)
export(countRead)
export(estGeno)
export(gbsrGDS2CSV)
export(gbsrGDS2VCF)
export(gbsrVCF2GDS)
export(getAlleleA)
export(getAlleleB)
export(getChromosome)
export(getCountAlleleAlt)
export(getCountAlleleMissing)
export(getCountAlleleRef)
export(getCountGenoAlt)
export(getCountGenoHet)
export(getCountGenoMissing)
export(getCountGenoRef)
export(getCountRead)
export(getCountReadAlt)
export(getCountReadRef)
export(getFlipped)
export(getGenotype)
export(getHaplotype)
export(getInfo)
export(getMAC)
export(getMAF)
export(getMeanReadAlt)
export(getMeanReadRef)
export(getParents)
export(getPloidy)
export(getPosition)
export(getQtileReadAlt)
export(getQtileReadRef)
export(getRead)
export(getSDReadAlt)
export(getSDReadRef)
export(getScanID)
export(getSnpID)
export(getValidScan)
export(getValidSnp)
export(hasFlipped)
export(histGBSR)
export(initScheme)
export(isOpenGDS)
export(loadGDS)
export(loadScanAnnot)
export(loadSnpAnnot)
export(nscan)
export(nsnp)
export(openGDS)
export(pairsGBSR)
export(plotDosage)
export(plotGBSR)
export(plotReadRatio)
export(resetFilters)
export(resetScanFilters)
export(resetSnpFilters)
export(saveScanAnnot)
export(saveSnpAnnot)
export(setCallFilter)
export(setFiltGenotype)
export(setInfoFilter)
export(setParents)
export(setRawGenotype)
export(setScanFilter)
export(setSnpFilter)
export(setValidScan)
export(setValidSnp)
export(showScheme)
export(subsetGDS)
export(thinMarker)
exportClasses(GbsrGenotypeData)
exportClasses(GbsrScheme)
importClassesFrom(GWASTools,GdsGenotypeReader)
importClassesFrom(GWASTools,GenotypeData)
importClassesFrom(GWASTools,ScanAnnotationDataFrame)
importClassesFrom(GWASTools,SnpAnnotationDataFrame)
importFrom(Biobase,"pData<-")
importFrom(Biobase,pData)
importFrom(GWASTools,GdsGenotypeReader)
importFrom(GWASTools,GenotypeData)
importFrom(GWASTools,ScanAnnotationDataFrame)
importFrom(GWASTools,SnpAnnotationDataFrame)
importFrom(GWASTools,getVariable)
importFrom(Rcpp,sourceCpp)
importFrom(RcppParallel,defaultNumThreads)
importFrom(RcppParallel,setThreadOptions)
importFrom(SeqArray,seqGDS2SNP)
importFrom(SeqArray,seqGDS2VCF)
importFrom(SeqArray,seqOpen)
importFrom(SeqArray,seqSNP2GDS)
importFrom(SeqArray,seqStorageOption)
importFrom(SeqArray,seqVCF2GDS)
importFrom(expm,expm.Higham08)
importFrom(gdsfmt,add.gdsn)
importFrom(gdsfmt,addfolder.gdsn)
importFrom(gdsfmt,append.gdsn)
importFrom(gdsfmt,apply.gdsn)
importFrom(gdsfmt,assign.gdsn)
importFrom(gdsfmt,closefn.gds)
importFrom(gdsfmt,compression.gdsn)
importFrom(gdsfmt,copyto.gdsn)
importFrom(gdsfmt,delete.gdsn)
importFrom(gdsfmt,diagnosis.gds)
importFrom(gdsfmt,exist.gdsn)
importFrom(gdsfmt,get.attr.gdsn)
importFrom(gdsfmt,index.gdsn)
importFrom(gdsfmt,ls.gdsn)
importFrom(gdsfmt,objdesp.gdsn)
importFrom(gdsfmt,openfn.gds)
importFrom(gdsfmt,put.attr.gdsn)
importFrom(gdsfmt,read.gdsn)
importFrom(gdsfmt,readex.gdsn)
importFrom(gdsfmt,readmode.gdsn)
importFrom(gdsfmt,rename.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_fill_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,new)
importFrom(methods,setClass)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(stats,cor)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(tidyr,pivot_longer)
importFrom(utils,head)
importFrom(utils,tail)
importFrom(utils,write.table)
importMethodsFrom(GWASTools,getScanAnnotation)
importMethodsFrom(GWASTools,getScanVariable)
importMethodsFrom(GWASTools,getSnpAnnotation)
importMethodsFrom(GWASTools,getSnpVariable)
importMethodsFrom(GWASTools,hasScanVariable)
importMethodsFrom(GWASTools,hasSnpVariable)
useDynLib(GBScleanR, .registration = TRUE)
