API for lvclark/polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Global functions
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
AddGenotypeLikelihood Man page Source code
AddGenotypeLikelihood.RADdata 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_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
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
AddPriorTimesLikelihood Man page Source code
AddPriorTimesLikelihood.RADdata Source code
AlleleProbExp Source code
BestGenos Source code
BestPloidies Source code
CanDoGetWeightedMeanGeno Man page Source code
CanDoGetWeightedMeanGeno.RADdata Source code
CheckAllelesPerLocus Source code
ClusterAlleles Source code
EstimateContaminationRate Man page Source code
EstimateContaminationRate.RADdata Man page Source code
ExportGAPIT Man page Source code
Export_TASSEL_Numeric Man page Source code
Export_polymapR 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
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
GetWeightedMeanGenotypes Man page Source code
GetWeightedMeanGenotypes.RADdata Man page Source code
HWEpriors 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
MakeTasselVcfFilter Man page Source code
MergeRareHaplotypes Man page Source code
MergeRareHaplotypes.RADdata Man page Source code
Msi01genes Man page
OneAllelePerMarker Man page Source code
OneAllelePerMarker.RADdata Man page Source code
PipelineMapping2Parents Man page Source code
RADdata 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
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
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
SubsetByTaxon Man page Source code
SubsetByTaxon.RADdata Man page Source code
ThirdDimProd Source code
VCF2RADdata Man page Source code
alleleFreq Source code
consolidateSNPs Source code
exampleRAD Man page
exampleRAD_mapping Man page
gameteProb Source code
gameteProbPop Source code
makeGametes Source code
mergeNucleotides Source code
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
ordered_gen_and_loctable Source code
print.RADdata Source code
priorTimesLikelihood Source code
progenyProb Source code
readHMC Man page Source code
readStacks Man page Source code
readTASSELGBSv2 Man page Source code
readTagDigger Man page Source code
selfPop Source code
selfmat Source code
lvclark/polyRAD documentation built on Oct. 3, 2018, 1:01 p.m.