MLE.ped {MasterBayes}R Documentation

Maximum Likelihood Estimation of the Pedigree

Description

Finds the MLE pedigree using the genetic data only. An approximation is used for genotyping error.

Usage

MLE.ped(X.list, ped=NULL, USdam=FALSE, nUSdam=NULL, USsire=FALSE, 
   nUSsire=NULL, threshold=0, ...)

Arguments

X.list list of design matrices for each offspring derived using getXlist
ped optional pedigree with id, dam and sire in ech column
USdam logical or character; if TRUE a single undiferentiated population of unsampled females exists. If USdam is a character vector it must have the same length as id with factor levels representing sub-populations (in time or space) over which the number of unsampled females vary.
nUSdam numeric vector for number of unsampled females
USsire logical or character; if TRUE a single undiferentiated population of unsampled males exists. If USsire is a character vector it must have the same length as id with factor levels representing sub-populations (in time or space) over which the number of unsampled males vary.
nUSsire numeric vector for number of unsampled males
threshold threshold probability under which ML parents are replaced by NA
... further arguments to be passed

Details

ML estimation of the pedigree is based on the Mendelian transition probabilities in the presence of genotyping error as outlined in Kalinwoski (2006). The probability that the ML parents are the true parents is simply the Mendelian transition probability for those parents divided by the sum of the transition probabilities for the remaining potential parents, both sampled and unsampled. If ped exists and the dam column contains known dam assignemnts and the sire column contains only NA's, then the ML sires will be returned conditional on the dam assignements being true. ML dam estimation with known sires can be performed in the same way. Individuals whose parents cannot be assigned with the required level of certainty (threshold), or whose parents belong to the base or unsampled population, have NA in the dan and sire columns.

Value

pedigree with id in the first column, and ML estimates for dam and sire in the second and third columns

Author(s)

Jarrod Hadfield j.hadfield@sheffield.ac.uk

References

Hadfield J.D. et al (2006) Molecular Ecology 15 3715-31 Marshall J.D. et al (1998) Molecular Ecology 7 639-655 Kalinowski S.T. et al, Molecular Ecology in press

See Also

MCMCped

Examples

data(WarblerP)
data(WarblerG)

GdP<-GdataPed(WarblerG)

res1<-expression(varPed("offspring", restrict=0))
res2<-expression(varPed("terr", gender="Female", relational="OFFSPRING", 
  restrict=TRUE))

PdP<-PdataPed(formula=list(res1,res2), data=WarblerP, USsire=TRUE)

X.list<-getXlist(PdP=PdP, GdP=GdP, E2=0.005)

ped<-MLE.ped(X.list, USsire=TRUE, nUSsire=10, threshold=0.75)

[Package MasterBayes version 1.0 Index]