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 |
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