AddGenotypePosteriorProb {polyRAD} | R Documentation |
Estimate Posterior Probabilities of Genotypes
Description
Given a "RADdata"
object containing genotype prior probabilities
and genotype likelihoods, this function estimates genotype posterior
probabilities and adds them to the $posteriorProb
slot of the object.
Usage
AddGenotypePosteriorProb(object, ...)
Arguments
object |
A |
... |
Potential future arguments (none currently in use). |
Value
A "RADdata"
object identical to that passed to the function, but
with a two-dimensional list added to the $posteriorProb
slot. Rows of
the list correspont to object$possiblePloidies
, and columns to unique
values in object$taxaPloidy
, similarly to object$priorProb
. Each
item of the list is a three dimensional array, with allele copy number in the
first dimension, taxa in the second dimension, and alleles in the third
dimension. For each allele and taxa, posterior probabilities will sum to one
across all potential allele copy numbers.
Author(s)
Lindsay V. Clark
See Also
AddGenotypeLikelihood
,
AddGenotypePriorProb_Mapping2Parents
Examples
# load dataset and set some parameters
data(exampleRAD_mapping)
exampleRAD_mapping <- SetDonorParent(exampleRAD_mapping, "parent1")
exampleRAD_mapping <- SetRecurrentParent(exampleRAD_mapping, "parent2")
exampleRAD_mapping <- AddAlleleFreqMapping(exampleRAD_mapping,
expectedFreqs = c(0.25, 0.75),
allowedDeviation = 0.08)
exampleRAD_mapping <- AddGenotypeLikelihood(exampleRAD_mapping)
exampleRAD_mapping <- AddGenotypePriorProb_Mapping2Parents(exampleRAD_mapping,
n.gen.backcrossing = 1)
# estimate posterior probabilities
exampleRAD_mapping <- AddGenotypePosteriorProb(exampleRAD_mapping)
# examine the results
exampleRAD_mapping$posteriorProb[[1,1]][,3,]