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:
polyRAD_2.0.0.9003.tar.gz
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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')) |
Bug tracker:https://github.com/lvclark/polyrad/issues
- Msi01genes - Miniature Datasets for Testing polyRAD Functions
- exampleRAD - Miniature Datasets for Testing polyRAD Functions
- exampleRAD_mapping - Miniature Datasets for Testing polyRAD Functions
bioinformaticsdna-sequencinggenotype-likelihoodsgenotyping-by-sequencinghacktoberfestrad-seqrad-sequencingsnp-genotyping
Last updated 11 months agofrom:6edf95b72e. Checks:OK: 3 NOTE: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 06 2024 |
| R-4.5-win-x86_64 | OK | Nov 06 2024 |
| R-4.5-linux-x86_64 | OK | Nov 06 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 06 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 06 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 06 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 06 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 06 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 06 2024 |
Exports:AddAlleleFreqByTaxaAddAlleleFreqHWEAddAlleleFreqMappingAddAlleleLinkagesAddDepthSamplingPermutationsAddGenotypeLikelihoodAddGenotypePosteriorProbAddGenotypePriorProb_ByTaxaAddGenotypePriorProb_EvenAddGenotypePriorProb_HWEAddGenotypePriorProb_LDAddGenotypePriorProb_Mapping2ParentsAddPCAAddPloidyChiSqAddPloidyLikelihoodCanDoGetWeightedMeanGenoEstimateContaminationRateEstimateParentalGenotypesExamineGenotypeExpectedHindHeExpectedHindHeMappingExport_adegenet_genindExport_GWASpolyExport_MAPpolyExport_polymapRExport_polymapR_probsExport_rrBLUP_AmatExport_rrBLUP_GWASExport_StructureExport_TASSEL_NumericExportGAPITGetAlleleNamesGetBlankTaxaGetContamRateGetDonorParentGetLikelyGenGetLocDepthGetLociGetProbableGenotypesGetRecurrentParentGetTaxaGetTaxaByPloidyGetTaxaPloidyGetWeightedMeanGenotypesHindHeHindHeMappingInbreedingFromHindHeIterateHWEIterateHWE_LDIteratePopStructIteratePopStructLDLocusInfoMakeTasselVcfFilterMergeIdenticalHaplotypesMergeRareHaplotypesMergeTaxaDepthnAllelesnLocinTaxaOneAllelePerMarkerPipelineMapping2ParentsRADdataRADdata2VCFreadDArTagreadHMCreadProcessIsolocireadProcessSamMultireadStacksreadTagDiggerreadTASSELGBSv2RemoveHighDepthLociRemoveMonomorphicLociRemoveUngenotypedLocireverseComplementSetBlankTaxaSetContamRateSetDonorParentSetRecurrentParentSetTaxaPloidySimAlleleDepthSimGenotypesSimGenotypesMappingSplitByChromosomeStripDownSubsetByLocusSubsetByPloidySubsetByTaxonTestOverdispersionVCF2RADdata
Dependencies:BiobaseBiocGenericsfastmatchgenericsMASSpcaMethodsRcppstringi
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Accessor Functions for RADdata Objects | GetAlleleNames GetContamRate GetLocDepth GetLoci GetTaxa GetTaxaByPloidy GetTaxaByPloidy.RADdata GetTaxaPloidy nAlleles nLoci nTaxa SetContamRate SetTaxaPloidy |
| Estimate Local Allele Frequencies for Each Taxon Based on Population Structure | AddAlleleFreqByTaxa AddAlleleFreqByTaxa.RADdata |
| Estimate Allele Frequencies in a RADdata Object Assuming Hardy-Weinberg Equilibrium | AddAlleleFreqHWE AddAlleleFreqHWE.RADdata |
| Estimate Allele Frequencies in a Mapping Population | AddAlleleFreqMapping AddAlleleFreqMapping.RADdata |
| Identify and Utilize Linked Alleles for Estimating Genotype Priors | AddAlleleLinkages AddAlleleLinkages.RADdata AddGenotypePriorProb_LD AddGenotypePriorProb_LD.RADdata |
| Estimate Genotype Likelihoods in a RADdata object | AddDepthSamplingPermutations AddGenotypeLikelihood AddGenotypeLikelihood.RADdata |
| Estimate Posterior Probabilities of Genotypes | AddGenotypePosteriorProb |
| Estimate Prior Genotype Probabilities on a Per-Taxon Basis | AddGenotypePriorProb_ByTaxa AddGenotypePriorProb_ByTaxa.RADdata |
| Add Uniform Priors to a RADdata Object | AddGenotypePriorProb_Even |
| Estimate Genotype Prior Probabilities In the Absence of Population Structure | AddGenotypePriorProb_HWE AddGenotypePriorProb_HWE.RADdata |
| Expected Genotype Frequencies in Mapping Populations | AddGenotypePriorProb_Mapping2Parents AddGenotypePriorProb_Mapping2Parents.RADdata EstimateParentalGenotypes EstimateParentalGenotypes.RADdata |
| Perform Principal Components Analysis on "RADdata" Object | AddPCA AddPCA.RADdata |
| Chi-Square Test on Genotype Likelihood Distributions | AddPloidyChiSq AddPloidyChiSq.RADdata |
| Likelihoods for Possible Ploidies Based on Genotype Distributions | AddPloidyLikelihood AddPloidyLikelihood.RADdata |
| Check Whether 'GetWeightedMeanGenotypes' Can Be Run | CanDoGetWeightedMeanGeno |
| Estimate Sample Contamination Using Blanks | EstimateContaminationRate EstimateContaminationRate.RADdata |
| Plots to Examine Genotype Calling at a Single Taxon and Allele | ExamineGenotype ExamineGenotype.RADdata |
| Miniature Datasets for Testing polyRAD Functions | exampleRAD exampleRAD_mapping Msi01genes |
| Simulate Data to Get Expected Distribution of Hind/He | ExpectedHindHe ExpectedHindHeMapping SimAlleleDepth SimGenotypes SimGenotypesMapping |
| Export RADdata Object for Use by Other R Packages | ExportGAPIT 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 Genotype | GetLikelyGen |
| Export Numeric Genotype Values from Posterior Probabilities | GetProbableGenotypes GetProbableGenotypes.RADdata GetWeightedMeanGenotypes GetWeightedMeanGenotypes.RADdata |
| Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations | HindHe HindHe.RADdata HindHeMapping HindHeMapping.RADdata |
| Estimate Inbreeding from Hind/He for a Given Ploidy | InbreedingFromHindHe |
| Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel | IterateHWE IterateHWE_LD IteratePopStruct IteratePopStructLD |
| Get Information about a Single Locus | LocusInfo LocusInfo.RADdata |
| Filter Lines of a VCF File By Call Rate and Allele Frequency | MakeTasselVcfFilter |
| Merge Alleles with Identical DNA Sequences | MergeIdenticalHaplotypes |
| Consolidate Reads from Rare Alleles | MergeRareHaplotypes MergeRareHaplotypes.RADdata |
| Combine Read Depths from Multiple Taxa into One Taxon | MergeTaxaDepth MergeTaxaDepth.RADdata |
| Return the Index of One Allele for Each Locus | OneAllelePerMarker OneAllelePerMarker.RADdata |
| Run polyRAD Pipeline on a Mapping Population | PipelineMapping2Parents |
| RADdata object constructor | plot.RADdata RADdata |
| Export RADdata Genotypes to VCF | RADdata2VCF |
| Import Data from DArT Sequencing | readDArTag |
| Import read depth from UNEAK | readHMC |
| Import Read Depth from Output of process_isoloci.py | readProcessIsoloci |
| Import Preliminary Data to Determine Parameters for Isolocus Sorting | readProcessSamMulti |
| Import Read Depth from Stacks | readStacks |
| Import Read Counts from TagDigger | readTagDigger |
| Import Read Depth and Alignment from TASSEL GBS v2 | readTASSELGBSv2 |
| Reverse Complement of DNA Sequence Stored as Character String | reverseComplement reverseComplement,character-method |
| Functions to Assign Taxa to Specific Roles | GetBlankTaxa GetDonorParent GetRecurrentParent SetBlankTaxa SetDonorParent SetRecurrentParent |
| Remove Unneeded Slots to Conserve Memory | StripDown StripDown.RADdata |
| Create RADdata Objects with a Subset of Loci | RemoveHighDepthLoci RemoveHighDepthLoci.RADdata RemoveMonomorphicLoci RemoveMonomorphicLoci.RADdata RemoveUngenotypedLoci RemoveUngenotypedLoci.RADdata SplitByChromosome SplitByChromosome.RADdata SubsetByLocus SubsetByLocus.RADdata |
| Create a RADdata object with a Subset of Possible Ploidies | SubsetByPloidy SubsetByPloidy.RADdata |
| Create RADdata Object with a Subset of Taxa | SubsetByTaxon SubsetByTaxon.RADdata |
| Test the Fit of Read Depth to Beta-Binomial Distribution | TestOverdispersion TestOverdispersion.RADdata |
| Create a RADdata Object from a VCF File | VCF2RADdata |
