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]