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polyRAD (version 1.1)

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. (2019) .

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Install

install.packages('polyRAD')

Monthly Downloads

442

Version

1.1

License

GPL (>= 2)

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Repository

https://github.com/lvclark/polyRAD

Maintainer

Lindsay V Clark

Last Published

June 4th, 2019

Functions in polyRAD (1.1)

AddGenotypeLikelihood

Estimate Genotype Likelihoods in a RADdata object

AddGenotypePosteriorProb

Estimate Posterior Probabilities of Genotypes

AddAlleleLinkages

Identify and Utilize Linked Alleles for Estimating Genotype Priors

AddAlleleFreqMapping

Estimate Allele Frequencies in a Mapping Population

AddAlleleFreqByTaxa

Estimate Local Allele Frequencies for Each Taxon Based on Population Structure

AddGenotypePriorProb_HWE

Estimate Genotype Prior Probabilities In the Absence of Population Structure

AddGenotypePriorProb_ByTaxa

Estimate Prior Genotype Probabilities on a Per-Taxon Basis

AddAlleleFreqHWE

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

AddGenotypePriorProb_Mapping2Parents

Expected Genotype Frequencies in Mapping Populations

AddGenotypePriorProb_Even

Add Uniform Priors to a RADdata Object

Perform Principal Components Analysis on “RADdata” Object

Chi-Square Test on Genotype Likelihood Distributions

Combine Read Depths from Multiple Taxa into One Taxon

AddPriorTimesLikelihood

Multiply Genotype Prior Probabilities by Genotype Likelihoods

AddPloidyLikelihood

Likelihoods for Possible Ploidies Based on Genotype Distributions

OneAllelePerMarker

Return the Index of One Allele for Each Locus

EstimateContaminationRate

Estimate Sample Contamination Using Blanks

CanDoGetWeightedMeanGeno

Check Whether GetWeightedMeanGenotypes Can Be Run

Import read depth from UNEAK

PipelineMapping2Parents

Run polyRAD Pipeline on a Mapping Population

RADdata object constructor

MakeTasselVcfFilter

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

MergeRareHaplotypes

Consolidate Reads from Rare Alleles

Import Read Depth from Stacks

Create RADdata Object with a Subset of Taxa

Export RADdata Object for Use by Other R Packages

GetWeightedMeanGenotypes

Export Numeric Genotype Values from Posterior Probabilities

Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel

Get Information about a Single Locus

Accessor Functions for RADdata Objects

Output the Most Likely Genotype

Create RADdata Objects with a Subset of Loci

Create a RADdata Object from a VCF File

readTASSELGBSv2

Import Read Depth and Alignment from TASSEL GBS v2

Functions to Assign Taxa to Specific Roles

Remove Unneeded Slots to Conserve Memory

TestOverdispersion

Test the Fit of Read Depth to Beta-Binomial Distribution

Create a RADdata object with a Subset of Possible Ploidies

Miniature Datasets for Testing polyRAD Functions

Import Read Counts from TagDigger