AddAlleleFreqByTaxa	AddAlleleFreqByTaxa
AddAlleleFreqByTaxa.RADdata	AddAlleleFreqByTaxa
AddAlleleFreqHWE	AddAlleleFreqHWE
AddAlleleFreqHWE.RADdata	AddAlleleFreqHWE
AddAlleleFreqMapping	AddAlleleFreqMapping
AddAlleleFreqMapping.RADdata	AddAlleleFreqMapping
AddAlleleLinkages	AddAlleleLinkages
AddAlleleLinkages.RADdata	AddAlleleLinkages
AddDepthSamplingPermutations	AddGenotypeLikelihood
AddGenotypeLikelihood	AddGenotypeLikelihood
AddGenotypeLikelihood.RADdata	AddGenotypeLikelihood
AddGenotypePosteriorProb	AddGenotypePosteriorProb
AddGenotypePriorProb_ByTaxa	AddGenotypePriorProb_ByTaxa
AddGenotypePriorProb_ByTaxa.RADdata	AddGenotypePriorProb_ByTaxa
AddGenotypePriorProb_Even	AddGenotypePriorProb_Even
AddGenotypePriorProb_HWE	AddGenotypePriorProb_HWE
AddGenotypePriorProb_HWE.RADdata	AddGenotypePriorProb_HWE
AddGenotypePriorProb_LD	AddAlleleLinkages
AddGenotypePriorProb_LD.RADdata	AddAlleleLinkages
AddGenotypePriorProb_Mapping2Parents	AddGenotypePriorProb_Mapping2Parents
AddGenotypePriorProb_Mapping2Parents.RADdata	AddGenotypePriorProb_Mapping2Parents
AddPCA	AddPCA
AddPCA.RADdata	AddPCA
AddPloidyChiSq	AddPloidyChiSq
AddPloidyChiSq.RADdata	AddPloidyChiSq
AddPloidyLikelihood	AddPloidyLikelihood
AddPloidyLikelihood.RADdata	AddPloidyLikelihood
CanDoGetWeightedMeanGeno	CanDoGetWeightedMeanGeno
EstimateContaminationRate	EstimateContaminationRate
EstimateContaminationRate.RADdata	EstimateContaminationRate
EstimateParentalGenotypes	AddGenotypePriorProb_Mapping2Parents
EstimateParentalGenotypes.RADdata	AddGenotypePriorProb_Mapping2Parents
ExamineGenotype	ExamineGenotype
ExamineGenotype.RADdata	ExamineGenotype
exampleRAD	exampleRAD
exampleRAD_mapping	exampleRAD
ExpectedHindHe	ExpectedHindHe
ExpectedHindHeMapping	ExpectedHindHe
ExportGAPIT	ExportGAPIT
Export_adegenet_genind	ExportGAPIT
Export_GWASpoly	ExportGAPIT
Export_MAPpoly	ExportGAPIT
Export_polymapR	ExportGAPIT
Export_polymapR_probs	ExportGAPIT
Export_rrBLUP_Amat	ExportGAPIT
Export_rrBLUP_GWAS	ExportGAPIT
Export_Structure	ExportGAPIT
Export_TASSEL_Numeric	ExportGAPIT
GetAlleleNames	GetTaxa
GetBlankTaxa	SetBlankTaxa
GetContamRate	GetTaxa
GetDonorParent	SetBlankTaxa
GetLikelyGen	GetLikelyGen
GetLocDepth	GetTaxa
GetLoci	GetTaxa
GetProbableGenotypes	GetWeightedMeanGenotypes
GetProbableGenotypes.RADdata	GetWeightedMeanGenotypes
GetRecurrentParent	SetBlankTaxa
GetTaxa	GetTaxa
GetTaxaByPloidy	GetTaxa
GetTaxaByPloidy.RADdata	GetTaxa
GetTaxaPloidy	GetTaxa
GetWeightedMeanGenotypes	GetWeightedMeanGenotypes
GetWeightedMeanGenotypes.RADdata	GetWeightedMeanGenotypes
HindHe	HindHe
HindHe.RADdata	HindHe
HindHeMapping	HindHe
HindHeMapping.RADdata	HindHe
InbreedingFromHindHe	InbreedingFromHindHe
IterateHWE	IterateHWE
IterateHWE_LD	IterateHWE
IteratePopStruct	IterateHWE
IteratePopStructLD	IterateHWE
LocusInfo	LocusInfo
LocusInfo.RADdata	LocusInfo
MakeTasselVcfFilter	MakeTasselVcfFilter
MergeIdenticalHaplotypes	MergeIdenticalHaplotypes
MergeRareHaplotypes	MergeRareHaplotypes
MergeRareHaplotypes.RADdata	MergeRareHaplotypes
MergeTaxaDepth	MergeTaxaDepth
MergeTaxaDepth.RADdata	MergeTaxaDepth
Msi01genes	exampleRAD
nAlleles	GetTaxa
nLoci	GetTaxa
nTaxa	GetTaxa
OneAllelePerMarker	OneAllelePerMarker
OneAllelePerMarker.RADdata	OneAllelePerMarker
PipelineMapping2Parents	PipelineMapping2Parents
plot.RADdata	RADdata
RADdata	RADdata
RADdata2VCF	RADdata2VCF
readDArTag	readDArTag
readHMC	readHMC
readProcessIsoloci	readProcessIsoloci
readProcessSamMulti	readProcessSamMulti
readStacks	readStacks
readTagDigger	readTagDigger
readTASSELGBSv2	readTASSELGBSv2
RemoveHighDepthLoci	SubsetByLocus
RemoveHighDepthLoci.RADdata	SubsetByLocus
RemoveMonomorphicLoci	SubsetByLocus
RemoveMonomorphicLoci.RADdata	SubsetByLocus
RemoveUngenotypedLoci	SubsetByLocus
RemoveUngenotypedLoci.RADdata	SubsetByLocus
reverseComplement	reverseComplement
reverseComplement,character-method	reverseComplement
SetBlankTaxa	SetBlankTaxa
SetContamRate	GetTaxa
SetDonorParent	SetBlankTaxa
SetRecurrentParent	SetBlankTaxa
SetTaxaPloidy	GetTaxa
SimAlleleDepth	ExpectedHindHe
SimGenotypes	ExpectedHindHe
SimGenotypesMapping	ExpectedHindHe
SplitByChromosome	SubsetByLocus
SplitByChromosome.RADdata	SubsetByLocus
StripDown	StripDown
StripDown.RADdata	StripDown
SubsetByLocus	SubsetByLocus
SubsetByLocus.RADdata	SubsetByLocus
SubsetByPloidy	SubsetByPloidy
SubsetByPloidy.RADdata	SubsetByPloidy
SubsetByTaxon	SubsetByTaxon
SubsetByTaxon.RADdata	SubsetByTaxon
TestOverdispersion	TestOverdispersion
TestOverdispersion.RADdata	TestOverdispersion
VCF2RADdata	VCF2RADdata
