Man pages for lvclark/polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
| AddAlleleFreqByTaxa | Estimate Local Allele Frequencies for Each Taxon Based on... |
| AddAlleleFreqHWE | Estimate Allele Frequencies in a RADdata Object Assuming... |
| AddAlleleFreqMapping | Estimate Allele Frequencies in a Mapping Population |
| AddAlleleLinkages | Identify and Utilize Linked Alleles for Estimating Genotype... |
| AddGenotypeLikelihood | 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_Even | Add Uniform Priors to a RADdata Object |
| AddGenotypePriorProb_HWE | Estimate Genotype Prior Probabilities In the Absence of... |
| AddGenotypePriorProb_Mapping2Parents | Expected Genotype Frequencies in Mapping Populations |
| AddPCA | Perform Principal Components Analysis on "RADdata" Object |
| AddPloidyChiSq | Chi-Square Test on Genotype Likelihood Distributions |
| AddPloidyLikelihood | Likelihoods for Possible Ploidies Based on Genotype... |
| CanDoGetWeightedMeanGeno | Check Whether 'GetWeightedMeanGenotypes' Can Be Run |
| EstimateContaminationRate | Estimate Sample Contamination Using Blanks |
| ExamineGenotype | Plots to Examine Genotype Calling at a Single Taxon and... |
| exampleRAD | Miniature Datasets for Testing polyRAD Functions |
| ExpectedHindHe | Simulate Data to Get Expected Distribution of Hind/He |
| ExportGAPIT | Export RADdata Object for Use by Other R Packages |
| GetLikelyGen | Output the Most Likely Genotype |
| GetTaxa | Accessor Functions for RADdata Objects |
| GetWeightedMeanGenotypes | Export Numeric Genotype Values from Posterior Probabilities |
| HindHe | Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy... |
| InbreedingFromHindHe | Estimate Inbreeding from Hind/He for a Given Ploidy |
| IterateHWE | Iteratively Estimate Population Parameters and Genotypes In a... |
| LocusInfo | Get Information about a Single Locus |
| 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 |
| MergeTaxaDepth | Combine Read Depths from Multiple Taxa into One Taxon |
| OneAllelePerMarker | Return the Index of One Allele for Each Locus |
| PipelineMapping2Parents | Run polyRAD Pipeline on a Mapping Population |
| 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... |
| readStacks | Import Read Depth from Stacks |
| readTagDigger | Import Read Counts from TagDigger |
| readTASSELGBSv2 | Import Read Depth and Alignment from TASSEL GBS v2 |
| reverseComplement | Reverse Complement of DNA Sequence Stored as Character String |
| SetBlankTaxa | Functions to Assign Taxa to Specific Roles |
| StripDown | Remove Unneeded Slots to Conserve Memory |
| SubsetByLocus | Create RADdata Objects with a Subset of Loci |
| SubsetByPloidy | Create a RADdata object with a Subset of Possible Ploidies |
| SubsetByTaxon | Create RADdata Object with a Subset of Taxa |
| TestOverdispersion | Test the Fit of Read Depth to Beta-Binomial Distribution |
| VCF2RADdata | Create a RADdata Object from a VCF File |
