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