Package: polyRAD 2.0.0.9003

Lindsay V. Clark

polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

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) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>. A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.

Authors:Lindsay V. Clark [aut, cre], U.S. National Science Foundation [fnd]

polyRAD_2.0.0.9003.tar.gz
polyRAD_2.0.0.9003.zip(r-4.5)polyRAD_2.0.0.9003.zip(r-4.4)polyRAD_2.0.0.9003.zip(r-4.3)
polyRAD_2.0.0.9003.tgz(r-4.4-arm64)polyRAD_2.0.0.9003.tgz(r-4.4-x86_64)polyRAD_2.0.0.9003.tgz(r-4.3-arm64)polyRAD_2.0.0.9003.tgz(r-4.3-x86_64)
polyRAD_2.0.0.9003.tar.gz(r-4.5-noble)polyRAD_2.0.0.9003.tar.gz(r-4.4-noble)
polyRAD_2.0.0.9003.tgz(r-4.4-emscripten)polyRAD_2.0.0.9003.tgz(r-4.3-emscripten)
polyRAD.pdf |polyRAD.html
polyRAD/json (API)
NEWS

# Install polyRAD in R:
install.packages('polyRAD', repos = c('https://polyploids.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lvclark/polyrad/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • Msi01genes - Miniature Datasets for Testing polyRAD Functions
  • exampleRAD - Miniature Datasets for Testing polyRAD Functions
  • exampleRAD_mapping - Miniature Datasets for Testing polyRAD Functions

On CRAN:

bioinformaticsdna-sequencinggenotype-likelihoodsgenotyping-by-sequencinghacktoberfestrad-seqrad-sequencingsnp-genotyping

89 exports 24 stars 2.32 score 7 dependencies 341 downloads

Last updated 6 months agofrom:6edf95b72ebf6962cc841fb9e6f089777029e6aa

Exports:AddAlleleFreqByTaxaAddAlleleFreqHWEAddAlleleFreqMappingAddAlleleLinkagesAddDepthSamplingPermutationsAddGenotypeLikelihoodAddGenotypePosteriorProbAddGenotypePriorProb_ByTaxaAddGenotypePriorProb_EvenAddGenotypePriorProb_HWEAddGenotypePriorProb_LDAddGenotypePriorProb_Mapping2ParentsAddPCAAddPloidyChiSqAddPloidyLikelihoodCanDoGetWeightedMeanGenoEstimateContaminationRateEstimateParentalGenotypesExamineGenotypeExpectedHindHeExpectedHindHeMappingExport_adegenet_genindExport_GWASpolyExport_MAPpolyExport_polymapRExport_polymapR_probsExport_rrBLUP_AmatExport_rrBLUP_GWASExport_StructureExport_TASSEL_NumericExportGAPITGetAlleleNamesGetBlankTaxaGetContamRateGetDonorParentGetLikelyGenGetLocDepthGetLociGetProbableGenotypesGetRecurrentParentGetTaxaGetTaxaByPloidyGetTaxaPloidyGetWeightedMeanGenotypesHindHeHindHeMappingInbreedingFromHindHeIterateHWEIterateHWE_LDIteratePopStructIteratePopStructLDLocusInfoMakeTasselVcfFilterMergeIdenticalHaplotypesMergeRareHaplotypesMergeTaxaDepthnAllelesnLocinTaxaOneAllelePerMarkerPipelineMapping2ParentsRADdataRADdata2VCFreadDArTagreadHMCreadProcessIsolocireadProcessSamMultireadStacksreadTagDiggerreadTASSELGBSv2RemoveHighDepthLociRemoveMonomorphicLociRemoveUngenotypedLocireverseComplementSetBlankTaxaSetContamRateSetDonorParentSetRecurrentParentSetTaxaPloidySimAlleleDepthSimGenotypesSimGenotypesMappingSplitByChromosomeStripDownSubsetByLocusSubsetByPloidySubsetByTaxonTestOverdispersionVCF2RADdata

Dependencies:BiobaseBiocGenericsfastmatchMASSpcaMethodsRcppstringi

polyRAD Tutorial

Rendered frompolyRADtutorial.Rmdusingknitr::rmarkdownon Jun 09 2024.

Last update: 2022-10-02
Started: 2018-06-08

Variant and Genotype Calling in Highly Duplicated Genomes

Rendered fromisolocus_sorting.Rmdusingknitr::rmarkdownon Jun 09 2024.

Last update: 2022-11-06
Started: 2019-11-03

Readme and manuals

Help Manual

Help pageTopics
Accessor Functions for RADdata ObjectsGetAlleleNames GetContamRate GetLocDepth GetLoci GetTaxa GetTaxaByPloidy GetTaxaByPloidy.RADdata GetTaxaPloidy nAlleles nLoci nTaxa SetContamRate SetTaxaPloidy
Estimate Local Allele Frequencies for Each Taxon Based on Population StructureAddAlleleFreqByTaxa AddAlleleFreqByTaxa.RADdata
Estimate Allele Frequencies in a RADdata Object Assuming Hardy-Weinberg EquilibriumAddAlleleFreqHWE AddAlleleFreqHWE.RADdata
Estimate Allele Frequencies in a Mapping PopulationAddAlleleFreqMapping AddAlleleFreqMapping.RADdata
Identify and Utilize Linked Alleles for Estimating Genotype PriorsAddAlleleLinkages AddAlleleLinkages.RADdata AddGenotypePriorProb_LD AddGenotypePriorProb_LD.RADdata
Estimate Genotype Likelihoods in a RADdata objectAddDepthSamplingPermutations AddGenotypeLikelihood AddGenotypeLikelihood.RADdata
Estimate Posterior Probabilities of GenotypesAddGenotypePosteriorProb
Estimate Prior Genotype Probabilities on a Per-Taxon BasisAddGenotypePriorProb_ByTaxa AddGenotypePriorProb_ByTaxa.RADdata
Add Uniform Priors to a RADdata ObjectAddGenotypePriorProb_Even
Estimate Genotype Prior Probabilities In the Absence of Population StructureAddGenotypePriorProb_HWE AddGenotypePriorProb_HWE.RADdata
Expected Genotype Frequencies in Mapping PopulationsAddGenotypePriorProb_Mapping2Parents AddGenotypePriorProb_Mapping2Parents.RADdata EstimateParentalGenotypes EstimateParentalGenotypes.RADdata
Perform Principal Components Analysis on "RADdata" ObjectAddPCA AddPCA.RADdata
Chi-Square Test on Genotype Likelihood DistributionsAddPloidyChiSq AddPloidyChiSq.RADdata
Likelihoods for Possible Ploidies Based on Genotype DistributionsAddPloidyLikelihood AddPloidyLikelihood.RADdata
Check Whether 'GetWeightedMeanGenotypes' Can Be RunCanDoGetWeightedMeanGeno
Estimate Sample Contamination Using BlanksEstimateContaminationRate EstimateContaminationRate.RADdata
Plots to Examine Genotype Calling at a Single Taxon and AlleleExamineGenotype ExamineGenotype.RADdata
Miniature Datasets for Testing polyRAD FunctionsexampleRAD exampleRAD_mapping Msi01genes
Simulate Data to Get Expected Distribution of Hind/HeExpectedHindHe ExpectedHindHeMapping SimAlleleDepth SimGenotypes SimGenotypesMapping
Export RADdata Object for Use by Other R PackagesExportGAPIT Export_adegenet_genind Export_GWASpoly Export_MAPpoly Export_polymapR Export_polymapR_probs Export_rrBLUP_Amat Export_rrBLUP_GWAS Export_Structure Export_TASSEL_Numeric
Output the Most Likely GenotypeGetLikelyGen
Export Numeric Genotype Values from Posterior ProbabilitiesGetProbableGenotypes GetProbableGenotypes.RADdata GetWeightedMeanGenotypes GetWeightedMeanGenotypes.RADdata
Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy ExpectationsHindHe HindHe.RADdata HindHeMapping HindHeMapping.RADdata
Estimate Inbreeding from Hind/He for a Given PloidyInbreedingFromHindHe
Iteratively Estimate Population Parameters and Genotypes In a Diversity PanelIterateHWE IterateHWE_LD IteratePopStruct IteratePopStructLD
Get Information about a Single LocusLocusInfo LocusInfo.RADdata
Filter Lines of a VCF File By Call Rate and Allele FrequencyMakeTasselVcfFilter
Merge Alleles with Identical DNA SequencesMergeIdenticalHaplotypes
Consolidate Reads from Rare AllelesMergeRareHaplotypes MergeRareHaplotypes.RADdata
Combine Read Depths from Multiple Taxa into One TaxonMergeTaxaDepth MergeTaxaDepth.RADdata
Return the Index of One Allele for Each LocusOneAllelePerMarker OneAllelePerMarker.RADdata
Run polyRAD Pipeline on a Mapping PopulationPipelineMapping2Parents
RADdata object constructorplot.RADdata RADdata
Export RADdata Genotypes to VCFRADdata2VCF
Import Data from DArT SequencingreadDArTag
Import read depth from UNEAKreadHMC
Import Read Depth from Output of process_isoloci.pyreadProcessIsoloci
Import Preliminary Data to Determine Parameters for Isolocus SortingreadProcessSamMulti
Import Read Depth from StacksreadStacks
Import Read Counts from TagDiggerreadTagDigger
Import Read Depth and Alignment from TASSEL GBS v2readTASSELGBSv2
Reverse Complement of DNA Sequence Stored as Character StringreverseComplement reverseComplement,character-method
Functions to Assign Taxa to Specific RolesGetBlankTaxa GetDonorParent GetRecurrentParent SetBlankTaxa SetDonorParent SetRecurrentParent
Remove Unneeded Slots to Conserve MemoryStripDown StripDown.RADdata
Create RADdata Objects with a Subset of LociRemoveHighDepthLoci RemoveHighDepthLoci.RADdata RemoveMonomorphicLoci RemoveMonomorphicLoci.RADdata RemoveUngenotypedLoci RemoveUngenotypedLoci.RADdata SplitByChromosome SplitByChromosome.RADdata SubsetByLocus SubsetByLocus.RADdata
Create a RADdata object with a Subset of Possible PloidiesSubsetByPloidy SubsetByPloidy.RADdata
Create RADdata Object with a Subset of TaxaSubsetByTaxon SubsetByTaxon.RADdata
Test the Fit of Read Depth to Beta-Binomial DistributionTestOverdispersion TestOverdispersion.RADdata
Create a RADdata Object from a VCF FileVCF2RADdata