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polyRAD (version 1.3)

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

355

Version

1.3

License

GPL (>= 2)

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Repository

https://github.com/lvclark/polyRAD

Maintainer

Lindsay V Clark

Last Published

January 6th, 2021

Functions in polyRAD (1.3)

AddGenotypePosteriorProb

Estimate Posterior Probabilities of Genotypes

AddGenotypePriorProb_HWE

Estimate Genotype Prior Probabilities In the Absence of Population Structure

AddAlleleFreqMapping

Estimate Allele Frequencies in a Mapping Population

AddAlleleLinkages

Identify and Utilize Linked Alleles for Estimating Genotype Priors

AddAlleleFreqHWE

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

AddAlleleFreqByTaxa

Estimate Local Allele Frequencies for Each Taxon Based on Population Structure

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

AddGenotypePriorProb_ByTaxa

Estimate Prior Genotype Probabilities on a Per-Taxon Basis

Perform Principal Components Analysis on “RADdata” Object

Chi-Square Test on Genotype Likelihood Distributions

Accessor Functions for RADdata Objects

Output the Most Likely Genotype

EstimateContaminationRate

Estimate Sample Contamination Using Blanks

Simulate Data to Get Expected Distribution of Hind/He

MakeTasselVcfFilter

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

AddPloidyLikelihood

Likelihoods for Possible Ploidies Based on Genotype Distributions

Export RADdata Object for Use by Other R Packages

AddPriorTimesLikelihood

Multiply Genotype Prior Probabilities by Genotype Likelihoods

MergeIdenticalHaplotypes

Merge Alleles with Identical DNA Sequences

Get Information about a Single Locus

MergeRareHaplotypes

Consolidate Reads from Rare Alleles

CanDoGetWeightedMeanGeno

Check Whether GetWeightedMeanGenotypes Can Be Run

Combine Read Depths from Multiple Taxa into One Taxon

OneAllelePerMarker

Return the Index of One Allele for Each Locus

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

GetWeightedMeanGenotypes

Export Numeric Genotype Values from Posterior Probabilities

Remove Unneeded Slots to Conserve Memory

Create RADdata Objects with a Subset of Loci

Functions to Assign Taxa to Specific Roles

Export RADdata Genotypes to VCF

readProcessIsoloci

Import Read Depth from Output of process_isoloci.py

readProcessSamMulti

Import Preliminary Data to Determine Parameters for Isolocus Sorting

PipelineMapping2Parents

Run polyRAD Pipeline on a Mapping Population

readTASSELGBSv2

Import Read Depth and Alignment from TASSEL GBS v2

Import Read Depth from Stacks

RADdata object constructor

Import Read Counts from TagDigger

Create a RADdata Object from a VCF File

TestOverdispersion

Test the Fit of Read Depth to Beta-Binomial Distribution

Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel

Miniature Datasets for Testing polyRAD Functions

Import read depth from UNEAK

Create a RADdata object with a Subset of Possible Ploidies

InbreedingFromHindHe

Estimate Inbreeding from Hind/He for a Given Ploidy

Create RADdata Object with a Subset of Taxa