legalG {MasterBayes}R Documentation

Legal Genotype Configurations

Description

A function for checking whether a set of genotypes have a positive probability given the pedigree. If not, a legal configuration is found using heuristic methods. Missing genotypes are also replaced with compatible genotypes.

Usage

legalG(G, A, ped, time_born=NULL, marker.type="MS", ...)

Arguments

G list of genotype objects
A list of allele frequencies
ped pedigree with id in the first column, dam in the second, and sire in the third. The genotypes must be in the same order as the id column
time_born an optional vector for ordering a pedigree more efficiently (see orderPed)
marker.type "MS" or "AFLP" for codominant or dominant markers respectively
... further arguments to be passed

Value

G a list of genotype objects with positive likelihood given the pedigree
legal logical; TRUE if the the genotype configuration passed to legalG had a positive likelihood

Author(s)

Jarrod Hadfield j.hadfield@ed.ac.uk

See Also

MCMCped

Examples

data(WarblerG)
A<-extractA(WarblerG[,16:17])

pedigree<-matrix(NA, 8,3)
pedigree[,1]<-1:8
pedigree[,2][5:8]<-c(1,1,2,2)
pedigree[,3][5:8]<-c(3,3,4,4)

G<-simgenotypes(A, E1=0, E2=0.3, pedigree=pedigree, no_dup=1)

newG<-legalG(G=G$Gobs,A=A,ped=pedigree)
newG$valid

# The input genotypes had a zero probability given the pedigree 
# (because of genotype error) but the outout genotypes have 
# positive probability

legalG(newG$G,A,pedigree)$valid

[Package MasterBayes version 2.42 Index]