API for lvclark/polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
| Global functions | |
|---|---|
| .HWEpriors | Source code |
| .alleleFreq | Source code |
| .buildProgProb | Source code |
| .chromosome_to_integer | Source code |
| .consolProgProb | Source code |
| .gameteProb | Source code |
| .gameteProbPop | Source code |
| .makeGametes | Source code |
| .makeGametes2 | Source code |
| .mergeNucleotides | Source code |
| .nucdist | Source code |
| .ordered_gen_and_loctable | Source code |
| .priorTimesLikelihood | Source code |
| .progAlProbs | Source code |
| .progenyProb | Source code |
| .progenyProb2 | Source code |
| .selfPop | Source code |
| .selfmat | Source code |
| AddAlleleBias | Source code |
| AddAlleleBias.RADdata | Source code |
| AddAlleleFreqByTaxa | Man page Source code |
| AddAlleleFreqByTaxa.RADdata | Man page Source code |
| AddAlleleFreqHWE | Man page Source code |
| AddAlleleFreqHWE.RADdata | Man page Source code |
| AddAlleleFreqMapping | Man page Source code |
| AddAlleleFreqMapping.RADdata | Man page Source code |
| AddAlleleLinkages | Man page Source code |
| AddAlleleLinkages.RADdata | Man page Source code |
| AddDepthSamplingPermutations | Man page Source code |
| AddDepthSamplingPermutations.RADdata | Source code |
| AddGenotypeLikelihood | Man page Source code |
| AddGenotypeLikelihood.RADdata | Man page Source code |
| AddGenotypePosteriorProb | Man page Source code |
| AddGenotypePosteriorProb.RADdata | Source code |
| AddGenotypePriorProb_ByTaxa | Man page Source code |
| AddGenotypePriorProb_ByTaxa.RADdata | Man page Source code |
| AddGenotypePriorProb_Even | Man page Source code |
| AddGenotypePriorProb_Even.RADdata | Source code |
| AddGenotypePriorProb_HWE | Man page Source code |
| AddGenotypePriorProb_HWE.RADdata | Man page Source code |
| AddGenotypePriorProb_LD | Man page Source code |
| AddGenotypePriorProb_LD.RADdata | Man page Source code |
| AddGenotypePriorProb_Mapping2Parents | Man page Source code |
| AddGenotypePriorProb_Mapping2Parents.RADdata | Man page Source code |
| AddNormalizedDepthProp | Source code |
| AddNormalizedDepthProp.RADdata | Source code |
| AddPCA | Man page Source code |
| AddPCA.RADdata | Man page Source code |
| AddPloidyChiSq | Man page Source code |
| AddPloidyChiSq.RADdata | Man page Source code |
| AddPloidyLikelihood | Man page Source code |
| AddPloidyLikelihood.RADdata | Man page Source code |
| AdjustAlleleFreq | Source code |
| BestGenos | Source code |
| BestPloidies | Source code |
| CanDoGetWeightedMeanGeno | Man page Source code |
| CanDoGetWeightedMeanGeno.RADdata | Source code |
| CorrectGenos | Source code |
| EstimateContaminationRate | Man page Source code |
| EstimateContaminationRate.RADdata | Man page Source code |
| EstimateParentalGenotypes | Man page Source code |
| EstimateParentalGenotypes.RADdata | Man page Source code |
| ExamineGenotype | Man page Source code |
| ExamineGenotype.RADdata | Man page Source code |
| ExpectedHindHe | Man page Source code |
| ExpectedHindHeMapping | Man page Source code |
| ExportGAPIT | Man page Source code |
| Export_GWASpoly | Man page Source code |
| Export_MAPpoly | Man page Source code |
| Export_Structure | Man page Source code |
| Export_TASSEL_Numeric | Man page Source code |
| Export_adegenet_genind | Man page Source code |
| Export_polymapR | Man page Source code |
| Export_polymapR_probs | Man page Source code |
| Export_rrBLUP_Amat | Man page Source code |
| Export_rrBLUP_GWAS | Man page Source code |
| FindNearbyAlleles | Source code |
| FindNearbyAlleles.RADdata | Source code |
| FormatStructure | Source code |
| GetAlleleNames | Man page Source code |
| GetAlleleNames.RADdata | Source code |
| GetBlankTaxa | Man page Source code |
| GetBlankTaxa.RADdata | Source code |
| GetContamRate | Man page Source code |
| GetContamRate.RADdata | Source code |
| GetDonorParent | Man page Source code |
| GetDonorParent.RADdata | Source code |
| GetLikelyGen | Man page Source code |
| GetLikelyGen.RADdata | Source code |
| GetLocDepth | Man page Source code |
| GetLocDepth.RADdata | Source code |
| GetLoci | Man page Source code |
| GetLoci.RADdata | Source code |
| GetProbableGenotypes | Man page Source code |
| GetProbableGenotypes.RADdata | Man page Source code |
| GetRecurrentParent | Man page Source code |
| GetRecurrentParent.RADdata | Source code |
| GetTaxa | Man page Source code |
| GetTaxa.RADdata | Source code |
| GetTaxaByPloidy | Man page Source code |
| GetTaxaByPloidy.RADdata | Man page Source code |
| GetTaxaPloidy | Man page Source code |
| GetTaxaPloidy.RADdata | Source code |
| GetWeightedMeanGenotypes | Man page Source code |
| GetWeightedMeanGenotypes.RADdata | Man page Source code |
| GiniSimpson | Source code |
| Hap2Hap | Source code |
| Hap2SNP | Source code |
| HindHe | Man page Source code |
| HindHe.RADdata | Man page Source code |
| HindHeMapping | Man page Source code |
| HindHeMapping.RADdata | Man page Source code |
| HindHeMat | Source code |
| HoOneParent | Source code |
| HoTwoParents | Source code |
| InbreedingFromHindHe | Man page Source code |
| InitHapAssign | Source code |
| IterateHWE | Man page Source code |
| IterateHWE_LD | Man page Source code |
| IteratePopStruct | Man page Source code |
| IteratePopStructLD | Man page Source code |
| LocusInfo | Man page Source code |
| LocusInfo.RADdata | Man page Source code |
| MakeGTstring | Source code |
| MakeTasselVcfFilter | Man page Source code |
| MergeIdenticalHaplotypes | Man page Source code |
| MergeIdenticalHaplotypes.RADdata | Source code |
| MergeRareHaplotypes | Man page Source code |
| MergeRareHaplotypes.RADdata | Man page Source code |
| MergeTaxaDepth | Man page Source code |
| MergeTaxaDepth.RADdata | Man page Source code |
| Msi01genes | Man page |
| OneAllelePerMarker | Man page Source code |
| OneAllelePerMarker.RADdata | Man page Source code |
| PipelineMapping2Parents | Man page Source code |
| PrepVCFexport | Source code |
| RADdata | Man page Source code |
| RADdata2VCF | Man page Source code |
| RemoveHighDepthLoci | Man page Source code |
| RemoveHighDepthLoci.RADdata | Man page Source code |
| RemoveMonomorphicLoci | Man page Source code |
| RemoveMonomorphicLoci.RADdata | Man page Source code |
| RemoveUngenotypedLoci | Man page Source code |
| RemoveUngenotypedLoci.RADdata | Man page Source code |
| SetBlankTaxa | Man page Source code |
| SetBlankTaxa.RADdata | Source code |
| SetContamRate | Man page Source code |
| SetContamRate.RADdata | Source code |
| SetDonorParent | Man page Source code |
| SetDonorParent.RADdata | Source code |
| SetRecurrentParent | Man page Source code |
| SetRecurrentParent.RADdata | Source code |
| SetTaxaPloidy | Man page Source code |
| SetTaxaPloidy.RADdata | Source code |
| SimAlleleDepth | Man page Source code |
| SimGenotypes | Man page Source code |
| SimGenotypesMapping | Man page Source code |
| SplitByChromosome | Man page Source code |
| SplitByChromosome.RADdata | Man page Source code |
| StripDown | Man page Source code |
| StripDown.RADdata | Man page Source code |
| SubsetByLocus | Man page Source code |
| SubsetByLocus.RADdata | Man page Source code |
| SubsetByPloidy | Man page Source code |
| SubsetByPloidy.RADdata | Man page Source code |
| SubsetByTaxon | Man page Source code |
| SubsetByTaxon.RADdata | Man page Source code |
| TestOverdispersion | Man page Source code |
| TestOverdispersion.RADdata | Man page Source code |
| ThirdDimProd | Source code |
| VCF2RADdata | Man page Source code |
| consolidateSNPs | Source code |
| exampleRAD | Man page |
| exampleRAD_mapping | Man page |
| nAlleles | Man page Source code |
| nAlleles.RADdata | Source code |
| nLoci | Man page Source code |
| nLoci.RADdata | Source code |
| nTaxa | Man page Source code |
| nTaxa.RADdata | Source code |
| plot.RADdata | Man page Source code |
| print.RADdata | Source code |
| readDArTag | Man page Source code |
| readHMC | Man page Source code |
| readProcessIsoloci | Man page Source code |
| readProcessSamMulti | Man page Source code |
| readStacks | Man page Source code |
| readTASSELGBSv2 | Man page Source code |
| readTagDigger | Man page Source code |
| reverseComplement | Man page |
| reverseComplement,character-method | Man page |
| simAD | Source code |
| simGeno | Source code |
| simGenoMapping | Source code |
