# Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

## Documentation for package ‘polyRAD’ version 1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

AddAlleleFreqByTaxa | Estimate Local Allele Frequencies for Each Taxon Based on Population Structure
AddAlleleFreqByTaxa.RADdata | Estimate Local Allele Frequencies for Each Taxon Based on Population Structure
AddAlleleFreqHWE | Estimate Allele Frequencies in a RADdata Object Assuming Hardy-Weinberg Equilibrium
AddAlleleFreqHWE.RADdata | Estimate Allele Frequencies in a RADdata Object Assuming Hardy-Weinberg Equilibrium
AddAlleleFreqMapping | Estimate Allele Frequencies in a Mapping Population
AddAlleleFreqMapping.RADdata | Estimate Allele Frequencies in a Mapping Population
AddAlleleLinkages | Identify and Utilize Linked Alleles for Estimating Genotype Priors
AddAlleleLinkages.RADdata | Identify and Utilize Linked Alleles for Estimating Genotype Priors
AddGenotypeLikelihood | Estimate Genotype Likelihoods in a RADdata object
AddGenotypeLikelihood.RADdata | 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_ByTaxa.RADdata | 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_HWE.RADdata | Estimate Genotype Prior Probabilities In the Absence of Population Structure
AddGenotypePriorProb_LD | Identify and Utilize Linked Alleles for Estimating Genotype Priors
AddGenotypePriorProb_LD.RADdata | Identify and Utilize Linked Alleles for Estimating Genotype Priors
AddGenotypePriorProb_Mapping2Parents | Expected Genotype Frequencies in Mapping Populations
AddGenotypePriorProb_Mapping2Parents.RADdata | Expected Genotype Frequencies in Mapping Populations
AddPCA | Perform Principal Components Analysis on "RADdata" Object
AddPCA.RADdata | Perform Principal Components Analysis on "RADdata" Object
AddPloidyChiSq | Chi-Square Test on Genotype Likelihood Distributions
AddPloidyChiSq.RADdata | Chi-Square Test on Genotype Likelihood Distributions
AddPloidyLikelihood | Likelihoods for Possible Ploidies Based on Genotype Distributions
AddPloidyLikelihood.RADdata | Likelihoods for Possible Ploidies Based on Genotype Distributions
AddPriorTimesLikelihood | Multiply Genotype Prior Probabilities by Genotype Likelihoods
CanDoGetWeightedMeanGeno | Check Whether 'GetWeightedMeanGenotypes' Can Be Run
EstimateContaminationRate | Estimate Sample Contamination Using Blanks
EstimateContaminationRate.RADdata | Estimate Sample Contamination Using Blanks
exampleRAD | Miniature Datasets for Testing polyRAD Functions
exampleRAD_mapping | Miniature Datasets for Testing polyRAD Functions
ExportGAPIT | Export RADdata Object for Use by Other R Packages
Export_GWASpoly | Export RADdata Object for Use by Other R Packages
Export_MAPpoly | Export RADdata Object for Use by Other R Packages
Export_polymapR | Export RADdata Object for Use by Other R Packages
Export_rrBLUP_Amat | Export RADdata Object for Use by Other R Packages
Export_rrBLUP_GWAS | Export RADdata Object for Use by Other R Packages
Export_TASSEL_Numeric | Export RADdata Object for Use by Other R Packages
GetAlleleNames | Accessor Functions for RADdata Objects
GetBlankTaxa | Functions to Assign Taxa to Specific Roles
GetContamRate | Accessor Functions for RADdata Objects
GetDonorParent | Functions to Assign Taxa to Specific Roles
GetLikelyGen | Output the Most Likely Genotype
GetLocDepth | Accessor Functions for RADdata Objects
GetLoci | Accessor Functions for RADdata Objects
GetProbableGenotypes | Export Numeric Genotype Values from Posterior Probabilities
GetProbableGenotypes.RADdata | Export Numeric Genotype Values from Posterior Probabilities
GetRecurrentParent | Functions to Assign Taxa to Specific Roles
GetTaxa | Accessor Functions for RADdata Objects
GetWeightedMeanGenotypes | Export Numeric Genotype Values from Posterior Probabilities
GetWeightedMeanGenotypes.RADdata | Export Numeric Genotype Values from Posterior Probabilities
IterateHWE | Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel
IterateHWE_LD | Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel
IteratePopStruct | Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel
IteratePopStructLD | Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel
LocusInfo | Get Information about a Single Locus
LocusInfo.RADdata | Get Information about a Single Locus
MakeTasselVcfFilter | Filter Lines of a VCF File By Call Rate and Allele Frequency
MergeRareHaplotypes | Consolidate Reads from Rare Alleles
MergeRareHaplotypes.RADdata | Consolidate Reads from Rare Alleles
MergeTaxaDepth | Combine Read Depths from Multiple Taxa into One Taxon
MergeTaxaDepth.RADdata | Combine Read Depths from Multiple Taxa into One Taxon
Msi01genes | Miniature Datasets for Testing polyRAD Functions
nAlleles | Accessor Functions for RADdata Objects
nLoci | Accessor Functions for RADdata Objects
nTaxa | Accessor Functions for RADdata Objects
OneAllelePerMarker | Return the Index of One Allele for Each Locus
OneAllelePerMarker.RADdata | Return the Index of One Allele for Each Locus
PipelineMapping2Parents | Run polyRAD Pipeline on a Mapping Population
plot.RADdata | RADdata object constructor
RADdata | RADdata object constructor
readHMC | Import read depth from UNEAK
readStacks | Import Read Depth from Stacks
readTagDigger | Import Read Counts from TagDigger
readTASSELGBSv2 | Import Read Depth and Alignment from TASSEL GBS v2
RemoveHighDepthLoci | Create RADdata Objects with a Subset of Loci
RemoveHighDepthLoci.RADdata | Create RADdata Objects with a Subset of Loci
RemoveMonomorphicLoci | Create RADdata Objects with a Subset of Loci
RemoveMonomorphicLoci.RADdata | Create RADdata Objects with a Subset of Loci
RemoveUngenotypedLoci | Create RADdata Objects with a Subset of Loci
RemoveUngenotypedLoci.RADdata | Create RADdata Objects with a Subset of Loci
SetBlankTaxa | Functions to Assign Taxa to Specific Roles
SetContamRate | Accessor Functions for RADdata Objects
SetDonorParent | Functions to Assign Taxa to Specific Roles
SetRecurrentParent | Functions to Assign Taxa to Specific Roles
SplitByChromosome | Create RADdata Objects with a Subset of Loci
SplitByChromosome.RADdata | Create RADdata Objects with a Subset of Loci
StripDown | Remove Unneeded Slots to Conserve Memory
StripDown.RADdata | Remove Unneeded Slots to Conserve Memory
SubsetByLocus | Create RADdata Objects with a Subset of Loci
SubsetByLocus.RADdata | Create RADdata Objects with a Subset of Loci
SubsetByPloidy | Create a RADdata object with a Subset of Possible Ploidies
SubsetByPloidy.RADdata | Create a RADdata object with a Subset of Possible Ploidies
SubsetByTaxon | Create RADdata Object with a Subset of Taxa
SubsetByTaxon.RADdata | Create RADdata Object with a Subset of Taxa
TestOverdispersion | Test the Fit of Read Depth to Beta-Binomial Distribution
TestOverdispersion.RADdata | Test the Fit of Read Depth to Beta-Binomial Distribution
VCF2RADdata | Create a RADdata Object from a VCF File