mismatches {MasterBayes} | R Documentation

## 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
`...` | further arguments to be passed

### 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 j.hadfield@sheffield.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), 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)

[Package MasterBayes version 2.0 Index]