# NOT RUN {
# 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)
exampleRAD_mapping <- AddGenotypePosteriorProb(exampleRAD_mapping)
exampleRAD_mapping <- AddPloidyChiSq(exampleRAD_mapping)
# get weighted mean genotypes
wmg <- GetWeightedMeanGenotypes(exampleRAD_mapping)
# examine the results
wmg[1:10,]
# get most probable genotypes
pg <- GetProbableGenotypes(exampleRAD_mapping, naIfZeroReads = TRUE)
# examine the results
pg$genotypes[1:10,]
# }
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