AddGenotypePriorProb_ByTaxa {polyRAD} | R Documentation |
Estimate Prior Genotype Probabilities on a Per-Taxon Basis
Description
Using local allele frequencies estimated by AddAlleleFreqByTaxa
and assuming Hardy-Weinberg Equilibruim or inbreeding on a local scale,
AddGenotypePriorProb_ByTaxa
estimates prior genotype probabilities at
each taxon, allele, and possible ploidy. These are then stored in the
$priorProb
slot of the "RADdata"
object.
Usage
AddGenotypePriorProb_ByTaxa(object, ...)
## S3 method for class 'RADdata'
AddGenotypePriorProb_ByTaxa(object, selfing.rate = 0, ...)
Arguments
object |
A |
selfing.rate |
A number ranging from zero to one indicating the frequency of self-fertilization in the species. |
... |
Additional arguments (none implemented). |
Value
A "RADdata"
object identical to that passed to the function, but with a
two-dimensional list added to the $priorProb
slot. Each row in the list
corresponds to one ploidy in object$possiblePloidies
, and each column
to a unique ploidy in object$taxaPloidy
. Each item is a three-dimensional
array with
allele copy number in the first dimension, taxa in the second dimension, and
alleles in the third dimension. The values in the array are prior genotype
probabilities. Additionally, "taxon"
is recorded in the
"priorType"
attribute.
Author(s)
Lindsay V. Clark
See Also
AddGenotypePriorProb_HWE
for equations used for genotype prior
probability estimation.
AddGenotypePriorProb_Mapping2Parents
,
AddGenotypeLikelihood
Examples
# load data
data(exampleRAD)
# do PCA
exampleRAD <- AddPCA(exampleRAD, nPcsInit = 3)
# get allele frequencies
exampleRAD <- AddAlleleFreqByTaxa(exampleRAD)
# add prior probabilities
exampleRAD <- AddGenotypePriorProb_ByTaxa(exampleRAD)
exampleRAD$priorProb[[1,1]][,1,]
exampleRAD$priorProb[[2,1]][,1,]
exampleRAD$priorProb[[1,1]][,2,]
exampleRAD$priorProb[[2,1]][,2,]
exampleRAD$priorProb[[1,2]][,1,]
# try it with inbreeding, for diploid samples only
exampleRAD2 <- SubsetByTaxon(exampleRAD, GetTaxa(exampleRAD)[exampleRAD$taxaPloidy == 2])
exampleRAD2 <- AddGenotypePriorProb_ByTaxa(exampleRAD2, selfing.rate = 0.5)
exampleRAD2$priorProb[[1,1]][,1,]