legalG: Legal Genotype Configurations

In MasterBayes: ML and MCMC Methods for Pedigree Reconstruction and Analysis

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="MSW")

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	"MSW" or "MSC" for co-dominant markers with Wang's (2004) model of genotyping error or CERVUS's model of genotyping error (Kalinowski, 2006; Marshall, 1998) or "AFLP" for dominant markers (Hadfield, 2009).

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 [e-mail]

References

Marshall, T. C. et al (1998) Molecular Ecology 7 5 639-655 Kalinowski S.T. et al (2007) Molecular Ecology 16 5 1099-1106 Hadfield J. D. et al (2009) in prep

See Also

MCMCped

Examples

## Not run: 
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, ped=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 output genotypes have 
# positive probability

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

## End(Not run)

MasterBayes documentation built on June 22, 2022, 5:06 p.m.