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polyRAD (version 1.0)

Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Description

Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, or genotypes sampled from those probabilties, can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2018) .

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Version

Install

install.packages('polyRAD')

Monthly Downloads

319

Version

1.0

License

GPL (>= 2)

Issues

3

Pull Requests

0

Stars

30

Forks

9

Maintainer

Lindsay V Clark

Last Published

November 19th, 2018

Functions in polyRAD (1.0)

AddAlleleFreqMapping

Estimate Allele Frequencies in a Mapping Population
GetWeightedMeanGenotypes

Export Numeric Genotype Values from Posterior Probabilities
MakeTasselVcfFilter

Filter Lines of a VCF File By Call Rate and Allele Frequency
AddAlleleFreqByTaxa

Estimate Local Allele Frequencies for Each Taxon Based on Population Structure
AddAlleleFreqHWE

Estimate Allele Frequencies in a RADdata Object Assuming Hardy-Weinberg Equilibrium
AddPCA

Perform Principal Components Analysis on “RADdata” Object
AddPloidyChiSq

Chi-Square Test on Genotype Likelihood Distributions
SubsetByTaxon

Create RADdata Object with a Subset of Taxa
MergeRareHaplotypes

Consolidate Reads from Rare Alleles
AddGenotypePriorProb_ByTaxa

Estimate Prior Genotype Probabilities on a Per-Taxon Basis
TestOverdispersion

Test the Fit of Read Depth to Beta-Binomial Distribution
IterateHWE

Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel
AddGenotypeLikelihood

Estimate Genotype Likelihoods in a RADdata object
LocusInfo

Get Information about a Single Locus
EstimateContaminationRate

Estimate Sample Contamination Using Blanks
AddGenotypePosteriorProb

Estimate Posterior Probabilities of Genotypes
CanDoGetWeightedMeanGeno

Check Whether GetWeightedMeanGenotypes Can Be Run
readTASSELGBSv2

Import Read Depth and Alignment from TASSEL GBS v2
readTagDigger

Import Read Counts from TagDigger
AddGenotypePriorProb_Even

Add Uniform Priors to a RADdata Object
ExportGAPIT

Export RADdata Object for Use by Other R Packages
GetLikelyGen

Output the Most Likely Genotype
OneAllelePerMarker

Return the Index of One Allele for Each Locus
StripDown

Remove Unneeded Slots to Conserve Memory
AddGenotypePriorProb_HWE

Estimate Genotype Prior Probabilities In the Absence of Population Structure
SubsetByLocus

Create RADdata Objects with a Subset of Loci
PipelineMapping2Parents

Run polyRAD Pipeline on a Mapping Population
AddGenotypePriorProb_Mapping2Parents

Expected Genotype Frequencies in Mapping Populations
AddPloidyLikelihood

Likelihoods for Possible Ploidies Based on Genotype Distributions
AddPriorTimesLikelihood

Multiply Genotype Prior Probabilities by Genotype Likelihoods
readHMC

Import read depth from UNEAK
readStacks

Import Read Depth from Stacks
RADdata

RADdata object constructor
SetBlankTaxa

Functions to Assign Taxa to Specific Roles
VCF2RADdata

Create a RADdata Object from a VCF File
exampleRAD

Miniature Datasets for Testing polyRAD Functions
AddAlleleLinkages

Identify and Utilize Linked Alleles for Estimating Genotype Priors
Accessors

Accessor Functions for RADdata Objects