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polyRAD (version 1.6)

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, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) . A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020) .

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Install

install.packages('polyRAD')

Monthly Downloads

315

Version

1.6

License

GPL (>= 2)

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Repository

https://github.com/lvclark/polyRAD

Maintainer

Lindsay V Clark

Last Published

February 15th, 2022

Functions in polyRAD (1.6)

AddGenotypeLikelihood

Estimate Genotype Likelihoods in a RADdata object

AddGenotypePriorProb_Even

Add Uniform Priors to a RADdata Object

AddAlleleFreqHWE

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

AddAlleleLinkages

Identify and Utilize Linked Alleles for Estimating Genotype Priors

AddGenotypePriorProb_HWE

Estimate Genotype Prior Probabilities In the Absence of Population Structure

AddGenotypePriorProb_ByTaxa

Estimate Prior Genotype Probabilities on a Per-Taxon Basis

AddAlleleFreqMapping

Estimate Allele Frequencies in a Mapping Population

Output the Most Likely Genotype

AddGenotypePosteriorProb

Estimate Posterior Probabilities of Genotypes

AddAlleleFreqByTaxa

Estimate Local Allele Frequencies for Each Taxon Based on Population Structure

AddGenotypePriorProb_Mapping2Parents

Expected Genotype Frequencies in Mapping Populations

Simulate Data to Get Expected Distribution of Hind/He

Export RADdata Object for Use by Other R Packages

MergeIdenticalHaplotypes

Merge Alleles with Identical DNA Sequences

MergeRareHaplotypes

Consolidate Reads from Rare Alleles

Accessor Functions for RADdata Objects

Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations

AddPloidyLikelihood

Likelihoods for Possible Ploidies Based on Genotype Distributions

GetWeightedMeanGenotypes

Export Numeric Genotype Values from Posterior Probabilities

Combine Read Depths from Multiple Taxa into One Taxon

AddPriorTimesLikelihood

Multiply Genotype Prior Probabilities by Genotype Likelihoods

Perform Principal Components Analysis on “RADdata” Object

InbreedingFromHindHe

Estimate Inbreeding from Hind/He for a Given Ploidy

OneAllelePerMarker

Return the Index of One Allele for Each Locus

Remove Unneeded Slots to Conserve Memory

PipelineMapping2Parents

Run polyRAD Pipeline on a Mapping Population

Export RADdata Genotypes to VCF

Functions to Assign Taxa to Specific Roles

RADdata object constructor

readProcessSamMulti

Import Preliminary Data to Determine Parameters for Isolocus Sorting

Create a RADdata object with a Subset of Possible Ploidies

Create RADdata Objects with a Subset of Loci

Chi-Square Test on Genotype Likelihood Distributions

Create RADdata Object with a Subset of Taxa

Import read depth from UNEAK

readProcessIsoloci

Import Read Depth from Output of process_isoloci.py

Import Read Depth from Stacks

CanDoGetWeightedMeanGeno

Check Whether GetWeightedMeanGenotypes Can Be Run

Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel

reverseComplement

Reverse Complement of DNA Sequence Stored as Character String

Import Data from DArT Sequencing

Import Read Counts from TagDigger

Miniature Datasets for Testing polyRAD Functions

readTASSELGBSv2

Import Read Depth and Alignment from TASSEL GBS v2

Get Information about a Single Locus

EstimateContaminationRate

Estimate Sample Contamination Using Blanks

TestOverdispersion

Test the Fit of Read Depth to Beta-Binomial Distribution

MakeTasselVcfFilter

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

Create a RADdata Object from a VCF File