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

## Documentation for package ‘polyRAD’ version 2.0.0

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

## Help Pages

A C E G H I L M N O P R S T V

## -- A --

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
AddDepthSamplingPermutations | Estimate Genotype Likelihoods in a RADdata object
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

## -- C --

CanDoGetWeightedMeanGeno | Check Whether 'GetWeightedMeanGenotypes' Can Be Run

## -- E --

EstimateContaminationRate | Estimate Sample Contamination Using Blanks
EstimateContaminationRate.RADdata | Estimate Sample Contamination Using Blanks
EstimateParentalGenotypes | Expected Genotype Frequencies in Mapping Populations
EstimateParentalGenotypes.RADdata | Expected Genotype Frequencies in Mapping Populations
ExamineGenotype | Plots to Examine Genotype Calling at a Single Taxon and Allele
ExamineGenotype.RADdata | Plots to Examine Genotype Calling at a Single Taxon and Allele
exampleRAD | Miniature Datasets for Testing polyRAD Functions
exampleRAD_mapping | Miniature Datasets for Testing polyRAD Functions
ExpectedHindHe | Simulate Data to Get Expected Distribution of Hind/He
ExpectedHindHeMapping | Simulate Data to Get Expected Distribution of Hind/He
ExportGAPIT | Export RADdata Object for Use by Other R Packages
Export_adegenet_genind | 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_polymapR_probs | 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_Structure | Export RADdata Object for Use by Other R Packages
Export_TASSEL_Numeric | Export RADdata Object for Use by Other R Packages

## -- G --

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
GetTaxaByPloidy | Accessor Functions for RADdata Objects
GetTaxaByPloidy.RADdata | Accessor Functions for RADdata Objects
GetTaxaPloidy | Accessor Functions for RADdata Objects
GetWeightedMeanGenotypes | Export Numeric Genotype Values from Posterior Probabilities
GetWeightedMeanGenotypes.RADdata | Export Numeric Genotype Values from Posterior Probabilities

## -- H --

HindHe | Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations
HindHe.RADdata | Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations
HindHeMapping | Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations
HindHeMapping.RADdata | Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations

## -- I --

InbreedingFromHindHe | Estimate Inbreeding from Hind/He for a Given Ploidy
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

## -- L --

LocusInfo | Get Information about a Single Locus
LocusInfo.RADdata | Get Information about a Single Locus

## -- M --

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
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

## -- N --

nAlleles | Accessor Functions for RADdata Objects
nLoci | Accessor Functions for RADdata Objects
nTaxa | Accessor Functions for RADdata Objects

## -- O --

OneAllelePerMarker | Return the Index of One Allele for Each Locus
OneAllelePerMarker.RADdata | Return the Index of One Allele for Each Locus

## -- P --

PipelineMapping2Parents | Run polyRAD Pipeline on a Mapping Population
plot.RADdata | RADdata object constructor

## -- R --

RADdata | RADdata object constructor
RADdata2VCF | Export RADdata Genotypes to VCF
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
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
reverseComplement | Reverse Complement of DNA Sequence Stored as Character String
reverseComplement-method | Reverse Complement of DNA Sequence Stored as Character String

## -- S --

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
SetTaxaPloidy | Accessor Functions for RADdata Objects
SimAlleleDepth | Simulate Data to Get Expected Distribution of Hind/He
SimGenotypes | Simulate Data to Get Expected Distribution of Hind/He
SimGenotypesMapping | Simulate Data to Get Expected Distribution of Hind/He
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

## -- T --

TestOverdispersion | Test the Fit of Read Depth to Beta-Binomial Distribution
TestOverdispersion.RADdata | Test the Fit of Read Depth to Beta-Binomial Distribution

## -- V --

VCF2RADdata | Create a RADdata Object from a VCF File