# Generated by roxygen2: do not edit by hand

export("PCAalgorithm<-")
export("PCAmissingRate<-")
export("anchorId<-")
export("batch<-")
export("blockTypeId<-")
export("chrInfo<-")
export("cleanADMIXTUREFiles<-")
export("eigenCount<-")
export("eigenCountSyn<-")
export("fieldPopInRef<-")
export("fieldPopInfAnc<-")
export("fieldSubPop<-")
export("fileReferenceAnnotGDS<-")
export("fileReferenceGDS<-")
export("genoSource<-")
export("genoType<-")
export("inferenceType<-")
export("kList<-")
export("listPos<-")
export("minCov<-")
export("minProb<-")
export("nbSim<-")
export("np<-")
export("pRecomb<-")
export("paramAncestry<-")
export("pathADMIXTURE<-")
export("pathProfileGDS<-")
export("pcaList<-")
export("pedStudy<-")
export("phase<-")
export("phaseType<-")
export("posOffset<-")
export("prefix<-")
export("profileFile<-")
export("pruningMethod<-")
export("reference<-")
export("sampleRef<-")
export("seedADMIXTURE<-")
export("seqError<-")
export("seqErrorSyn<-")
export("slideWindowMaxBP<-")
export("specificSNV<-")
export("studyDF<-")
export("studyDFSyn<-")
export("studyType<-")
export("syntheticRefDF<-")
export("thresholdLD<-")
export("verbose<-")
export(PCAalgorithm)
export(PCAmissingRate)
export(RAIDSparam)
export(add1KG2SampleGDS)
export(addBlockFromDetFile)
export(addGeneBlockGDSRefAnnot)
export(addGeneBlockRefAnnot)
export(addGenotypeProfile)
export(addRef2GDS1KG)
export(addStudy1Kg)
export(ancestryInferencePCAKNN)
export(anchorId)
export(batch)
export(blockTypeId)
export(chrInfo)
export(cleanADMIXTUREFiles)
export(computeAdmixtureProportions)
export(computeAncestryFromSynthetic)
export(computeAncestryFromSynthetic2)
export(computeAncestryFromSyntheticFile)
export(computeKNNRefSample)
export(computeKNNRefSyn)
export(computeKNNRefSynthetic)
export(computePCAMultiSynthetic)
export(computePCARefSample)
export(computePoolSyntheticAncestryGr)
export(computePoolSyntheticAncestryGr2)
export(computeSyntheticROC)
export(createAUROCGraph)
export(createAccuracyGraph)
export(createStudy2GDS1KG)
export(eigenCount)
export(eigenCountSyn)
export(estimateAllelicFraction)
export(fieldPopInRef)
export(fieldPopInfAnc)
export(fieldSubPop)
export(fileReferenceAnnotGDS)
export(fileReferenceGDS)
export(generateGDS1KG)
export(generateMapSnvSel)
export(generatePhase1KG2GDS)
export(generatePhaseRef)
export(generateVCF)
export(genoSource)
export(genoType)
export(genome)
export(getMatrixPopSynthetic)
export(getRef1KGPop)
export(getRefSuperPop)
export(getRefSuperPop2)
export(groupChr1KGSNV)
export(identifyRelative)
export(identifyRelativeRef)
export(inferAncestry)
export(inferAncestryDNA)
export(inferAncestryGeneAware)
export(inferenceType)
export(kList)
export(listPos)
export(minCov)
export(minProb)
export(nbSim)
export(np)
export(pRecomb)
export(paramAncestry)
export(pathADMIXTURE)
export(pathProfileGDS)
export(pcaList)
export(pedStudy)
export(phase)
export(phaseType)
export(posOffset)
export(prefix)
export(prepPMatrix)
export(prepPed1KG)
export(prepPedSyntheticRef)
export(prepSynthetic)
export(profileFile)
export(profileGenoSynthesis)
export(pruningMethod)
export(pruningProfile2)
export(pruningSample)
export(reference)
export(runADMIXTURE)
export(runExomeAncestry)
export(runRNAAncestry)
export(runSynADMIXTURE)
export(sampleRef)
export(seedADMIXTURE)
export(select1KGPop)
export(select1KGPopForSynthetic)
export(selectForSynthetic)
export(seqError)
export(seqErrorSyn)
export(slideWindowMaxBP)
export(snvListVCF)
export(snvListVCFRef)
export(specificSNV)
export(splitSelectByPop)
export(studyDF)
export(studyDFSyn)
export(studyType)
export(syntheticGeno)
export(syntheticGeno2)
export(syntheticRefDF)
export(thresholdLD)
export(verbose)
export(writeBedProfile)
export(writeBimPruned)
export(writeFamProfile)
export(writePMatrix)
exportClasses(CharacterOrNULL)
exportClasses(DataFrameOrNULL)
exportClasses(RAIDSparam)
exportMethods("PCAalgorithm<-")
exportMethods("PCAmissingRate<-")
exportMethods("anchorId<-")
exportMethods("batch<-")
exportMethods("blockTypeId<-")
exportMethods("chrInfo<-")
exportMethods("cleanADMIXTUREFiles<-")
exportMethods("eigenCount<-")
exportMethods("eigenCountSyn<-")
exportMethods("fieldPopInRef<-")
exportMethods("fieldPopInfAnc<-")
exportMethods("fieldSubPop<-")
exportMethods("fileReferenceAnnotGDS<-")
exportMethods("fileReferenceGDS<-")
exportMethods("genoSource<-")
exportMethods("genoType<-")
exportMethods("inferenceType<-")
exportMethods("kList<-")
exportMethods("listPos<-")
exportMethods("minCov<-")
exportMethods("minProb<-")
exportMethods("nbSim<-")
exportMethods("np<-")
exportMethods("pRecomb<-")
exportMethods("paramAncestry<-")
exportMethods("pathADMIXTURE<-")
exportMethods("pathProfileGDS<-")
exportMethods("pcaList<-")
exportMethods("pedStudy<-")
exportMethods("phase<-")
exportMethods("phaseType<-")
exportMethods("posOffset<-")
exportMethods("prefix<-")
exportMethods("profileFile<-")
exportMethods("pruningMethod<-")
exportMethods("reference<-")
exportMethods("sampleRef<-")
exportMethods("seedADMIXTURE<-")
exportMethods("seqError<-")
exportMethods("seqErrorSyn<-")
exportMethods("slideWindowMaxBP<-")
exportMethods("specificSNV<-")
exportMethods("studyDF<-")
exportMethods("studyDFSyn<-")
exportMethods("studyType<-")
exportMethods("syntheticRefDF<-")
exportMethods("thresholdLD<-")
exportMethods("verbose<-")
exportMethods(PCAalgorithm)
exportMethods(PCAmissingRate)
exportMethods(anchorId)
exportMethods(batch)
exportMethods(blockTypeId)
exportMethods(chrInfo)
exportMethods(cleanADMIXTUREFiles)
exportMethods(eigenCount)
exportMethods(eigenCountSyn)
exportMethods(fieldPopInRef)
exportMethods(fieldPopInfAnc)
exportMethods(fieldSubPop)
exportMethods(fileReferenceAnnotGDS)
exportMethods(fileReferenceGDS)
exportMethods(genoSource)
exportMethods(genoType)
exportMethods(genome)
exportMethods(inferenceType)
exportMethods(kList)
exportMethods(listPos)
exportMethods(minCov)
exportMethods(minProb)
exportMethods(nbSim)
exportMethods(np)
exportMethods(pRecomb)
exportMethods(paramAncestry)
exportMethods(pathADMIXTURE)
exportMethods(pathProfileGDS)
exportMethods(pcaList)
exportMethods(pedStudy)
exportMethods(phase)
exportMethods(phaseType)
exportMethods(posOffset)
exportMethods(prefix)
exportMethods(profileFile)
exportMethods(pruningMethod)
exportMethods(reference)
exportMethods(sampleRef)
exportMethods(seedADMIXTURE)
exportMethods(seqError)
exportMethods(seqErrorSyn)
exportMethods(slideWindowMaxBP)
exportMethods(specificSNV)
exportMethods(studyDF)
exportMethods(studyDFSyn)
exportMethods(studyType)
exportMethods(syntheticRefDF)
exportMethods(thresholdLD)
exportMethods(verbose)
importFrom(AnnotationDbi,select)
importFrom(AnnotationFilter,GeneIdFilter)
importFrom(BSgenome,strand)
importFrom(BSgenome.Hsapiens.UCSC.hg38,Hsapiens)
importFrom(BiocParallel,
  MulticoreParam,
  bplapply
)
importFrom(GENESIS,pcairPartition)
importFrom(GenomicRanges,
  GRanges,
  reduce,
  seqnames,
  start,
  width
)
importFrom(IRanges,IRanges)
importFrom(MatrixGenerics,rowRanges)
importFrom(Rsamtools,
  BamFile,
  PileupParam,
  ScanBamParam,
  pileup
)
importFrom(S4Vectors,
  Rle,
  aggregate,
  isSingleNumber,
  isSingleString
)
importFrom(SNPRelate,
  snpgdsClose,
  snpgdsGetGeno,
  snpgdsIBDKING,
  snpgdsLDpruning,
  snpgdsOpen,
  snpgdsPCA,
  snpgdsPCASNPLoading,
  snpgdsPCASampLoading
)
importFrom(Seqinfo,seqlengths)
importFrom(VariantAnnotation,
  geno,
  readVcf
)
importFrom(class,knn)
importFrom(dplyr,
  "%>%",
  group_by,
  summarize
)
importFrom(ensembldb,
  exonsBy,
  genes,
  toSAF
)
importFrom(gdsfmt,
  add.gdsn,
  append.gdsn,
  closefn.gds,
  compression.gdsn,
  createfn.gds,
  delete.gdsn,
  index.gdsn,
  ls.gdsn,
  objdesp.gdsn,
  openfn.gds,
  put.attr.gdsn,
  read.gdsn,
  readmode.gdsn,
  sync.gds,
  write.gdsn
)
importFrom(genio,
  write_bed,
  write_bim,
  write_fam
)
importFrom(ggplot2,
  aes,
  element_rect,
  element_text,
  facet_grid,
  geom_line,
  geom_ribbon,
  ggplot,
  ggtitle,
  scale_colour_manual,
  theme,
  theme_classic,
  ylab,
  ylim
)
importFrom(methods,
  is,
  new,
  validObject
)
importFrom(pROC,
  multiclass.roc,
  roc
)
importFrom(philentropy,JSD)
importFrom(rlang,
  .data,
  arg_match
)
importFrom(stats,
  dbinom,
  mad,
  median,
  pbinom,
  qbinom,
  quantile,
  rmultinom
)
importFrom(stringr,str_detect)
importFrom(utils,
  read.csv,
  read.csv2,
  read.delim,
  write.csv,
  write.csv2,
  write.table
)
