| fillX.G {MasterBayes} | R Documentation |
This function is primarily intended for use within getXlist, and fills in the design matrices of the model with the genetic likelihoods. The model of genotyping error for codominant markers is taken from CERVUS (Kalinowski, 2006; Marshall, 1998), and the model for dominant markers is taken from (Hadfield, 2007).
fillX.G(X.list, A, G, E1=0.005, E2=0.005, marker.type="MS", ...)
X.list |
list of design matrices for each offspring derived using getXlist |
A |
list of allele frequencies |
G |
list of genotype objects; rows must correspond to individuals in the vector X.list$id |
E1 |
the probability of a dominant allele being scored as a recessive allele for dominant markers |
E2 |
per-allele genotyping error rate. E2(2-E2) is the per-genotype rate defined in Kalinowski (2006) for codominant markers, and E2 is the probability of a recessive allele being scored as a dominant allele for dominant markers |
marker.type |
"MS" or "AFLP" for codominant or dominant markers respectively |
... |
further arguments to be passed |
list of design matrices of the form X.list containing genetic likelihoods for each offspring.
If a GdataPed object is passed to getXlist then the genetic likelihoods will be calculated by default.
Jarrod Hadfield j.hadfield@ed.ac.uk
Kalinowski S.T. et al (2006) Molecular Ecology in press Hadfield J. D. et al (2007) in prep
data(WarblerG)
A<-extractA(WarblerG)
ped<-matrix(NA, 5,3)
ped[,1]<-1:5
ped[,2]<-c(rep(NA, 4), 1)
ped[,3]<-c(rep(NA, 4), 2)
genotypes<-simgenotypes(A, ped=ped)
sex<-c("Female", "Male", "Female", "Male","Female")
offspring<-c(0,0,0,0,1)
data<-data.frame(id=ped[,1], sex, offspring)
res1<-expression(varPed(x="offspring", restrict=0))
PdP<-PdataPed(formula=list(res1), data=data)
GdP<-GdataPed(G=genotypes$Gobs, id=genotypes$id)
X.list<-getXlist(PdP)
# creates design matrices for offspring (in this case indivdiual "5")
X.list.G<-fillX.G(X.list, A=A, G=genotypes$Gobs, E2=0.005)
# genetic likelihoods are arranged sires within dams
X.list.G$X$"5"$dam.id
X.list.G$X$"5"$sire.id
# so for this example we have parental combinations
# ("1","2"), ("1","4"), ("3","2"), ("2","4"):
X.list.G$X$"5"$G
# The true parents have the highest likelihood in this case