R: computes logLik of two blurGenotypes

getLogLikelihoodGivenRelation {GenABEL} | R Documentation

## computes logLik of two blurGenotypes

### Description

Compute logLik of genotypes of person 1 given genotypes of person 2 and assumed relation between the two persons (expressed with transition probability matrix; as returned with 'makeTransitionMatrix').

### Usage

      getLogLikelihoodGivenRelation(bGenotype1, bGenotype2,
        TransitionMatrix, q)

### Arguments

`bGenotype1` | blurred genotype of person 1
`bGenotype2` | blurred genotype of person 2
`TransitionMatrix` | transition probability matrix
`q` | vector of effect allele frequencies

### Author(s)

Yurii Aulchenko

### Examples

    require(GenABEL.data)
    data(srdta)
    # select 10 first SNPs
    df <- srdta[,1:10]
    # compute effect allele freq
    EAF <- summary(gtdata(df))$"Q.2"
    # get genotypes of first 2 people
    g1 <- as.numeric(df[1:2,])
    # blur all genotypes of person 1; use HWE to infer missing
    bg1 <- blurGenotype(g1[1,],q=EAF)
    # blur all genotypes of person 2; use HWE to infer missing
    bg2 <- blurGenotype(g1[2,],q=EAF)
    # generate sib-sib transision matrices
    trss <- makeTransitionMatrix(EAF,nmei=c(2,2))
    getLogLikelihoodGivenRelation(bg1,bg2,trss,EAF)

[Package GenABEL version 1.8-0 Index]