Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids
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Documentation for package ‘polyRAD’ version 2.0.0
Help Pages
-- A --
| AddAlleleFreqByTaxa | Estimate Local Allele Frequencies for Each Taxon Based on Population Structure |
| AddAlleleFreqByTaxa.RADdata | Estimate Local Allele Frequencies for Each Taxon Based on Population Structure |
| AddAlleleFreqHWE | Estimate Allele Frequencies in a RADdata Object Assuming Hardy-Weinberg Equilibrium |
| AddAlleleFreqHWE.RADdata | Estimate Allele Frequencies in a RADdata Object Assuming Hardy-Weinberg Equilibrium |
| AddAlleleFreqMapping | Estimate Allele Frequencies in a Mapping Population |
| AddAlleleFreqMapping.RADdata | Estimate Allele Frequencies in a Mapping Population |
| AddAlleleLinkages | Identify and Utilize Linked Alleles for Estimating Genotype Priors |
| AddAlleleLinkages.RADdata | Identify and Utilize Linked Alleles for Estimating Genotype Priors |
| AddDepthSamplingPermutations | Estimate Genotype Likelihoods in a RADdata object |
| AddGenotypeLikelihood | Estimate Genotype Likelihoods in a RADdata object |
| AddGenotypeLikelihood.RADdata | Estimate Genotype Likelihoods in a RADdata object |
| AddGenotypePosteriorProb | Estimate Posterior Probabilities of Genotypes |
| AddGenotypePriorProb_ByTaxa | Estimate Prior Genotype Probabilities on a Per-Taxon Basis |
| AddGenotypePriorProb_ByTaxa.RADdata | Estimate Prior Genotype Probabilities on a Per-Taxon Basis |
| AddGenotypePriorProb_Even | Add Uniform Priors to a RADdata Object |
| AddGenotypePriorProb_HWE | Estimate Genotype Prior Probabilities In the Absence of Population Structure |
| AddGenotypePriorProb_HWE.RADdata | Estimate Genotype Prior Probabilities In the Absence of Population Structure |
| AddGenotypePriorProb_LD | Identify and Utilize Linked Alleles for Estimating Genotype Priors |
| AddGenotypePriorProb_LD.RADdata | Identify and Utilize Linked Alleles for Estimating Genotype Priors |
| AddGenotypePriorProb_Mapping2Parents | Expected Genotype Frequencies in Mapping Populations |
| AddGenotypePriorProb_Mapping2Parents.RADdata | Expected Genotype Frequencies in Mapping Populations |
| AddPCA | Perform Principal Components Analysis on "RADdata" Object |
| AddPCA.RADdata | Perform Principal Components Analysis on "RADdata" Object |
| AddPloidyChiSq | Chi-Square Test on Genotype Likelihood Distributions |
| AddPloidyChiSq.RADdata | Chi-Square Test on Genotype Likelihood Distributions |
| AddPloidyLikelihood | Likelihoods for Possible Ploidies Based on Genotype Distributions |
| AddPloidyLikelihood.RADdata | Likelihoods for Possible Ploidies Based on Genotype Distributions |
-- C --
| CanDoGetWeightedMeanGeno | Check Whether 'GetWeightedMeanGenotypes' Can Be Run |
-- E --
| EstimateContaminationRate | Estimate Sample Contamination Using Blanks |
| EstimateContaminationRate.RADdata | Estimate Sample Contamination Using Blanks |
| EstimateParentalGenotypes | Expected Genotype Frequencies in Mapping Populations |
| EstimateParentalGenotypes.RADdata | Expected Genotype Frequencies in Mapping Populations |
| ExamineGenotype | Plots to Examine Genotype Calling at a Single Taxon and Allele |
| ExamineGenotype.RADdata | Plots to Examine Genotype Calling at a Single Taxon and Allele |
| exampleRAD | Miniature Datasets for Testing polyRAD Functions |
| exampleRAD_mapping | Miniature Datasets for Testing polyRAD Functions |
| ExpectedHindHe | Simulate Data to Get Expected Distribution of Hind/He |
| ExpectedHindHeMapping | Simulate Data to Get Expected Distribution of Hind/He |
| ExportGAPIT | Export RADdata Object for Use by Other R Packages |
| Export_adegenet_genind | Export RADdata Object for Use by Other R Packages |
| Export_GWASpoly | Export RADdata Object for Use by Other R Packages |
| Export_MAPpoly | Export RADdata Object for Use by Other R Packages |
| Export_polymapR | Export RADdata Object for Use by Other R Packages |
| Export_polymapR_probs | Export RADdata Object for Use by Other R Packages |
| Export_rrBLUP_Amat | Export RADdata Object for Use by Other R Packages |
| Export_rrBLUP_GWAS | Export RADdata Object for Use by Other R Packages |
| Export_Structure | Export RADdata Object for Use by Other R Packages |
| Export_TASSEL_Numeric | Export RADdata Object for Use by Other R Packages |
-- G --
| GetAlleleNames | Accessor Functions for RADdata Objects |
| GetBlankTaxa | Functions to Assign Taxa to Specific Roles |
| GetContamRate | Accessor Functions for RADdata Objects |
| GetDonorParent | Functions to Assign Taxa to Specific Roles |
| GetLikelyGen | Output the Most Likely Genotype |
| GetLocDepth | Accessor Functions for RADdata Objects |
| GetLoci | Accessor Functions for RADdata Objects |
| GetProbableGenotypes | Export Numeric Genotype Values from Posterior Probabilities |
| GetProbableGenotypes.RADdata | Export Numeric Genotype Values from Posterior Probabilities |
| GetRecurrentParent | Functions to Assign Taxa to Specific Roles |
| GetTaxa | Accessor Functions for RADdata Objects |
| GetTaxaByPloidy | Accessor Functions for RADdata Objects |
| GetTaxaByPloidy.RADdata | Accessor Functions for RADdata Objects |
| GetTaxaPloidy | Accessor Functions for RADdata Objects |
| GetWeightedMeanGenotypes | Export Numeric Genotype Values from Posterior Probabilities |
| GetWeightedMeanGenotypes.RADdata | Export Numeric Genotype Values from Posterior Probabilities |
-- H --
| HindHe | Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations |
| HindHe.RADdata | Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations |
| HindHeMapping | Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations |
| HindHeMapping.RADdata | Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations |
-- I --
| InbreedingFromHindHe | Estimate Inbreeding from Hind/He for a Given Ploidy |
| IterateHWE | Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel |
| IterateHWE_LD | Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel |
| IteratePopStruct | Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel |
| IteratePopStructLD | Iteratively Estimate Population Parameters and Genotypes In a Diversity Panel |
-- L --
| LocusInfo | Get Information about a Single Locus |
| LocusInfo.RADdata | Get Information about a Single Locus |
-- M --
| MakeTasselVcfFilter | Filter Lines of a VCF File By Call Rate and Allele Frequency |
| MergeIdenticalHaplotypes | Merge Alleles with Identical DNA Sequences |
| MergeRareHaplotypes | Consolidate Reads from Rare Alleles |
| MergeRareHaplotypes.RADdata | Consolidate Reads from Rare Alleles |
| MergeTaxaDepth | Combine Read Depths from Multiple Taxa into One Taxon |
| MergeTaxaDepth.RADdata | Combine Read Depths from Multiple Taxa into One Taxon |
| Msi01genes | Miniature Datasets for Testing polyRAD Functions |
-- N --
| nAlleles | Accessor Functions for RADdata Objects |
| nLoci | Accessor Functions for RADdata Objects |
| nTaxa | Accessor Functions for RADdata Objects |
-- O --
| OneAllelePerMarker | Return the Index of One Allele for Each Locus |
| OneAllelePerMarker.RADdata | Return the Index of One Allele for Each Locus |
-- P --
| PipelineMapping2Parents | Run polyRAD Pipeline on a Mapping Population |
| plot.RADdata | RADdata object constructor |
-- R --
| RADdata | RADdata object constructor |
| RADdata2VCF | Export RADdata Genotypes to VCF |
| readDArTag | Import Data from DArT Sequencing |
| readHMC | Import read depth from UNEAK |
| readProcessIsoloci | Import Read Depth from Output of process_isoloci.py |
| readProcessSamMulti | Import Preliminary Data to Determine Parameters for Isolocus Sorting |
| readStacks | Import Read Depth from Stacks |
| readTagDigger | Import Read Counts from TagDigger |
| readTASSELGBSv2 | Import Read Depth and Alignment from TASSEL GBS v2 |
| RemoveHighDepthLoci | Create RADdata Objects with a Subset of Loci |
| RemoveHighDepthLoci.RADdata | Create RADdata Objects with a Subset of Loci |
| RemoveMonomorphicLoci | Create RADdata Objects with a Subset of Loci |
| RemoveMonomorphicLoci.RADdata | Create RADdata Objects with a Subset of Loci |
| RemoveUngenotypedLoci | Create RADdata Objects with a Subset of Loci |
| RemoveUngenotypedLoci.RADdata | Create RADdata Objects with a Subset of Loci |
| reverseComplement | Reverse Complement of DNA Sequence Stored as Character String |
| reverseComplement-method | Reverse Complement of DNA Sequence Stored as Character String |
-- S --
| SetBlankTaxa | Functions to Assign Taxa to Specific Roles |
| SetContamRate | Accessor Functions for RADdata Objects |
| SetDonorParent | Functions to Assign Taxa to Specific Roles |
| SetRecurrentParent | Functions to Assign Taxa to Specific Roles |
| SetTaxaPloidy | Accessor Functions for RADdata Objects |
| SimAlleleDepth | Simulate Data to Get Expected Distribution of Hind/He |
| SimGenotypes | Simulate Data to Get Expected Distribution of Hind/He |
| SimGenotypesMapping | Simulate Data to Get Expected Distribution of Hind/He |
| SplitByChromosome | Create RADdata Objects with a Subset of Loci |
| SplitByChromosome.RADdata | Create RADdata Objects with a Subset of Loci |
| StripDown | Remove Unneeded Slots to Conserve Memory |
| StripDown.RADdata | Remove Unneeded Slots to Conserve Memory |
| SubsetByLocus | Create RADdata Objects with a Subset of Loci |
| SubsetByLocus.RADdata | Create RADdata Objects with a Subset of Loci |
| SubsetByPloidy | Create a RADdata object with a Subset of Possible Ploidies |
| SubsetByPloidy.RADdata | Create a RADdata object with a Subset of Possible Ploidies |
| SubsetByTaxon | Create RADdata Object with a Subset of Taxa |
| SubsetByTaxon.RADdata | Create RADdata Object with a Subset of Taxa |
-- T --
| TestOverdispersion | Test the Fit of Read Depth to Beta-Binomial Distribution |
| TestOverdispersion.RADdata | Test the Fit of Read Depth to Beta-Binomial Distribution |
-- V --
| VCF2RADdata | Create a RADdata Object from a VCF File |