AddAlleleFreqByTaxa     Estimate Local Allele Frequencies for Each
                        Taxon Based on Population Structure
AddAlleleFreqHWE        Estimate Allele Frequencies in a RADdata Object
                        Assuming Hardy-Weinberg Equilibrium
AddAlleleFreqMapping    Estimate Allele Frequencies in a Mapping
                        Population
AddAlleleLinkages       Identify and Utilize Linked Alleles for
                        Estimating Genotype Priors
AddGenotypeLikelihood   Estimate Genotype Likelihoods in a RADdata
                        object
AddGenotypePosteriorProb
                        Estimate Posterior Probabilities of Genotypes
AddGenotypePriorProb_ByTaxa
                        Estimate Prior Genotype Probabilities on a
                        Per-Taxon Basis
AddGenotypePriorProb_Even
                        Add Uniform Priors to a RADdata Object
AddGenotypePriorProb_HWE
                        Estimate Genotype Prior Probabilities In the
                        Absence of Population Structure
AddGenotypePriorProb_Mapping2Parents
                        Expected Genotype Frequencies in Mapping
                        Populations
AddPCA                  Perform Principal Components Analysis on
                        "RADdata" Object
AddPloidyChiSq          Chi-Square Test on Genotype Likelihood
                        Distributions
AddPloidyLikelihood     Likelihoods for Possible Ploidies Based on
                        Genotype Distributions
CanDoGetWeightedMeanGeno
                        Check Whether 'GetWeightedMeanGenotypes' Can Be
                        Run
EstimateContaminationRate
                        Estimate Sample Contamination Using Blanks
ExamineGenotype         Plots to Examine Genotype Calling at a Single
                        Taxon and Allele
ExpectedHindHe          Simulate Data to Get Expected Distribution of
                        Hind/He
ExportGAPIT             Export RADdata Object for Use by Other R
                        Packages
GetLikelyGen            Output the Most Likely Genotype
GetTaxa                 Accessor Functions for RADdata Objects
GetWeightedMeanGenotypes
                        Export Numeric Genotype Values from Posterior
                        Probabilities
HindHe                  Identify Non-Mendelian Loci and Taxa that
                        Deviate from Ploidy Expectations
InbreedingFromHindHe    Estimate Inbreeding from Hind/He for a Given
                        Ploidy
IterateHWE              Iteratively Estimate Population Parameters and
                        Genotypes In a Diversity Panel
LocusInfo               Get Information about a Single Locus
MakeTasselVcfFilter     Filter Lines of a VCF File By Call Rate and
                        Allele Frequency
MergeIdenticalHaplotypes
                        Merge Alleles with Identical DNA Sequences
MergeRareHaplotypes     Consolidate Reads from Rare Alleles
MergeTaxaDepth          Combine Read Depths from Multiple Taxa into One
                        Taxon
OneAllelePerMarker      Return the Index of One Allele for Each Locus
PipelineMapping2Parents
                        Run polyRAD Pipeline on a Mapping Population
RADdata                 RADdata object constructor
RADdata2VCF             Export RADdata Genotypes to VCF
SetBlankTaxa            Functions to Assign Taxa to Specific Roles
StripDown               Remove Unneeded Slots to Conserve Memory
SubsetByLocus           Create RADdata Objects with a Subset of Loci
SubsetByPloidy          Create a RADdata object with a Subset of
                        Possible Ploidies
SubsetByTaxon           Create RADdata Object with a Subset of Taxa
TestOverdispersion      Test the Fit of Read Depth to Beta-Binomial
                        Distribution
VCF2RADdata             Create a RADdata Object from a VCF File
exampleRAD              Miniature Datasets for Testing polyRAD
                        Functions
readDArTag              Import Data from DArT Sequencing
readHMC                 Import read depth from UNEAK
readProcessIsoloci      Import Read Depth from Output of
                        process_isoloci.py
readProcessSamMulti     Import Preliminary Data to Determine Parameters
                        for Isolocus Sorting
readStacks              Import Read Depth from Stacks
readTASSELGBSv2         Import Read Depth and Alignment from TASSEL GBS
                        v2
readTagDigger           Import Read Counts from TagDigger
reverseComplement       Reverse Complement of DNA Sequence Stored as
                        Character String
