Man pages for lvclark/polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

AddAlleleFreqByTaxaEstimate Local Allele Frequencies for Each Taxon Based on...
AddAlleleFreqHWEEstimate Allele Frequencies in a RADdata Object Assuming...
AddAlleleFreqMappingEstimate Allele Frequencies in a Mapping Population
AddAlleleLinkagesIdentify and Utilize Linked Alleles for Estimating Genotype...
AddGenotypeLikelihoodEstimate Genotype Likelihoods in a RADdata object
AddGenotypePosteriorProbEstimate Posterior Probabilities of Genotypes
AddGenotypePriorProb_ByTaxaEstimate Prior Genotype Probabilities on a Per-Taxon Basis
AddGenotypePriorProb_EvenAdd Uniform Priors to a RADdata Object
AddGenotypePriorProb_HWEEstimate Genotype Prior Probabilities In the Absence of...
AddGenotypePriorProb_Mapping2ParentsExpected Genotype Frequencies in Mapping Populations
AddPCAPerform Principal Components Analysis on "RADdata" Object
AddPloidyChiSqChi-Square Test on Genotype Likelihood Distributions
AddPloidyLikelihoodLikelihoods for Possible Ploidies Based on Genotype...
AddPriorTimesLikelihoodMultiply Genotype Prior Probabilities by Genotype Likelihoods
CanDoGetWeightedMeanGenoCheck Whether 'GetWeightedMeanGenotypes' Can Be Run
EstimateContaminationRateEstimate Sample Contamination Using Blanks
exampleRADMiniature Datasets for Testing polyRAD Functions
ExportGAPITExport RADdata Object for Use by Other R Packages
GetLikelyGenOutput the Most Likely Genotype
GetTaxaAccessor Functions for RADdata Objects
GetWeightedMeanGenotypesExport Numeric Genotype Values from Posterior Probabilities
IterateHWEIteratively Estimate Population Parameters and Genotypes In a...
LocusInfoGet Information about a Single Locus
MakeTasselVcfFilterFilter Lines of a VCF File By Call Rate and Allele Frequency
MergeRareHaplotypesConsolidate Reads from Rare Alleles
MergeTaxaDepthCombine Read Depths from Multiple Taxa into One Taxon
OneAllelePerMarkerReturn the Index of One Allele for Each Locus
PipelineMapping2ParentsRun polyRAD Pipeline on a Mapping Population
RADdataRADdata object constructor
readHMCImport read depth from UNEAK
readStacksImport Read Depth from Stacks
readTagDiggerImport Read Counts from TagDigger
readTASSELGBSv2Import Read Depth and Alignment from TASSEL GBS v2
SetBlankTaxaFunctions to Assign Taxa to Specific Roles
StripDownRemove Unneeded Slots to Conserve Memory
SubsetByLocusCreate RADdata Objects with a Subset of Loci
SubsetByPloidyCreate a RADdata object with a Subset of Possible Ploidies
SubsetByTaxonCreate RADdata Object with a Subset of Taxa
TestOverdispersionTest the Fit of Read Depth to Beta-Binomial Distribution
VCF2RADdataCreate a RADdata Object from a VCF File
lvclark/polyRAD documentation built on Aug. 16, 2019, 8:15 a.m.