reordXlist {MasterBayes}R Documentation

Reorders Design Matrices

Description

Reorders design matrices so excluded parents appear last, and high probability parents appear first, thus increasing computational efficiency.

Usage

  reordXlist(X.list, marker.type="MS", ...)

Arguments

X.list list of design matrices for each offspring derived using getXlist. Mismatch information must be present (see mismatches)
marker.type "MS" or "AFLP" for codominant or dominant markers respectively
... Further arguments to be passed

Details

The design matrices are reordered by the number of mismatches between a parent and offspring for codominant markers, and by the probability of the offspring genotype conditional on parent genotype for dominant markers.

Value

X.list for which parents are reordered

Note

If a GdataPed object is passed to getXlist then the design matrices will be reordered by default.

Author(s)

Jarrod Hadfield j.hadfield@ed.ac.uk

See Also

MCMCped

Examples

data(WarblerG)
A<-extractA(WarblerG)

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

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)

var1<-expression(varPed(x="offspring", restrict=0))
PdP<-PdataPed(formula=list(var1), data=data)

X.list<-getXlist(PdP)
# creates design matrices for offspring (in this case indivdiual "5")

X.list<-mismatches(X.list, G=genotypes$Gobs)
X.list<-fillX.G(X.list, A=A, G=genotypes$Gobs)

X.list.reord<-reordXlist(X.list)

# The design matrices for the genetic likelihoods are reordered
# by the number of mismatches.  The true parental combination
# now appears first rather than last.

X.list$X$"5"$G
X.list.reord$X$"5"$G

[Package MasterBayes version 2.42 Index]