mismatches: Parent-Offspring Genotype Mismatches

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

Parent-Offspring Genotype Mismatches

Description

Calculates the number of mismatches between parental and offspring genotypes, assuming the genotypes of spouses are unknown. Primarily intended to be used inside the function getXlist where potential parents can be excluded based on the number of mismatches. Dominant markers do not produce mismatches.

Usage

mismatches(X.list, G, mm.tol=999)

Arguments

X.list	list of design matrices for each offspring derived using getXlist
G	list of genotype objects, the rows of which must refer to the id vector X.list$id
mm.tol	maximum number of mismatches that are tolerated before exclusion

Value

list of design matrices of the form X.list, but containing the number of mismatches between parents and offspring. Potential parents that exceed the number of mismatches specified by mm.tol are removed from the vectors of potential parents: restdam.id and restsire.id.

Note

If a GdataPed object is passed to getXlist then the number of mismatches will be calculated by default.

Author(s)

Jarrod Hadfield [e-mail]

See Also

MCMCped

Examples

## Not run: 
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)

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

X.list.MM<-mismatches(X.list, G=genotypes$Gobs, mm.tol=0)
# genetic likelihoods are arranged sires within dams 

X.list.MM$X$"5"$mmD
# number of mismatches between offspring "5" and dams "1" and "3"

X.list.MM$X$"5"$mmS
# number of mismatches between offspring "5" and sires "4" and "5"

X.list.MM$X$"5"$restdam.id
X.list.MM$X$"5"$dam.id
# dams with mismatches are excluded  mismatch (mm.tol=0)

X.list.MM$X$"5"$restsire.id
X.list.MM$X$"5"$sire.id
# sires with mismatches are excluded  mismatch (mm.tol=0)

## End(Not run)

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