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polyRAD (version 2.0.0)

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, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) , and the Hind/He statistic for marker filtering is described by Clark et al. (2022) . A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) .

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Install

install.packages('polyRAD')

Monthly Downloads

315

Version

2.0.0

License

GPL (>= 2)

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Repository

https://github.com/lvclark/polyRAD

Maintainer

Lindsay V. Clark

Last Published

November 6th, 2022

Functions in polyRAD (2.0.0)

AddGenotypePriorProb_HWE

Estimate Genotype Prior Probabilities In the Absence of Population Structure

AddAlleleFreqMapping

Estimate Allele Frequencies in a Mapping Population

AddAlleleFreqHWE

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

AddAlleleFreqByTaxa

Estimate Local Allele Frequencies for Each Taxon Based on Population Structure

AddGenotypePosteriorProb

Estimate Posterior Probabilities of Genotypes

AddPloidyLikelihood

Likelihoods for Possible Ploidies Based on Genotype Distributions

AddAlleleLinkages

Identify and Utilize Linked Alleles for Estimating Genotype Priors

AddGenotypePriorProb_Even

Add Uniform Priors to a RADdata Object

AddGenotypeLikelihood

Estimate Genotype Likelihoods in a RADdata object

AddGenotypePriorProb_Mapping2Parents

Expected Genotype Frequencies in Mapping Populations

Simulate Data to Get Expected Distribution of Hind/He

EstimateContaminationRate

Estimate Sample Contamination Using Blanks

CanDoGetWeightedMeanGeno

Check Whether GetWeightedMeanGenotypes Can Be Run

Export RADdata Object for Use by Other R Packages

Get Information about a Single Locus

TestOverdispersion

Test the Fit of Read Depth to Beta-Binomial Distribution

Create a RADdata Object from a VCF File

AddGenotypePriorProb_ByTaxa

Estimate Prior Genotype Probabilities on a Per-Taxon Basis

ExamineGenotype

Plots to Examine Genotype Calling at a Single Taxon and Allele

MakeTasselVcfFilter

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

MergeIdenticalHaplotypes

Merge Alleles with Identical DNA Sequences

Perform Principal Components Analysis on “RADdata” Object

InbreedingFromHindHe

Estimate Inbreeding from Hind/He for a Given Ploidy

Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel

Chi-Square Test on Genotype Likelihood Distributions

Create a RADdata object with a Subset of Possible Ploidies

Import read depth from UNEAK

MergeRareHaplotypes

Consolidate Reads from Rare Alleles

Create RADdata Object with a Subset of Taxa

readProcessIsoloci

Import Read Depth from Output of process_isoloci.py

Export RADdata Genotypes to VCF

Remove Unneeded Slots to Conserve Memory

readProcessSamMulti

Import Preliminary Data to Determine Parameters for Isolocus Sorting

Functions to Assign Taxa to Specific Roles

Output the Most Likely Genotype

Import Read Depth from Stacks

Combine Read Depths from Multiple Taxa into One Taxon

OneAllelePerMarker

Return the Index of One Allele for Each Locus

readTASSELGBSv2

Import Read Depth and Alignment from TASSEL GBS v2

Accessor Functions for RADdata Objects

Import Read Counts from TagDigger

GetWeightedMeanGenotypes

Export Numeric Genotype Values from Posterior Probabilities

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

Create RADdata Objects with a Subset of Loci

reverseComplement

Reverse Complement of DNA Sequence Stored as Character String

PipelineMapping2Parents

Run polyRAD Pipeline on a Mapping Population

RADdata object constructor

Miniature Datasets for Testing polyRAD Functions

Import Data from DArT Sequencing