R: Get a list of objects for haplotype pairs

get.hapPair {haplo.stats} | R Documentation

## Get a list of objects for haplotype pairs

### Description

Get a list of objects for modeling haplotype pairs from a set of unique haplotypes and their frequencies, given the baseline haplotype

### Usage

    get.hapPair(haplo, haplo.freq, base.index)

### Arguments

`haplo` | matrix of haplotypes, with rows the different haplotypes and columns the alleles of the haplotypes. For H haplotypes of L loci, haplo has dimension H x L.
`haplo.freq` | vector of length H for the population haplotype frequencies (corresponding to the rows of haplo)
`base.index` | integer index of the haplotype considered to be the base-line for logistic regression (index between 1 and H); often, the most common haplotype is chosen for the base-line.

### Value

list with components:

`p.g` | Genotype probability under Hardy-Weinberg Equilibrium, where the genotype is the haplotype pair
`x.haplo` | Design matrix for all pairs of haplotypes, excluding the baseline haplotype. Effects are coded to an additive effect for the haplotypes.
`haplo.indx` | two-column matrix containing the indices for the haplotypes in x.haplo. The indices are the row of the haplotype in haplo.

### Examples

    haplo <- rbind(
                   c(     1,    2,    2,    1,    2),
                   c(     1,    2,    2,    1,    1),
                   c(     1,    1,    2,    1,    1),
                   c(     1,    2,    1,    1,    2),
                   c(     1,    2,    2,    2,    1),
                   c(     1,    2,    1,    1,    1),
                   c(     1,    1,    2,    2,    1),
                   c(     1,    1,    1,    1,    2),
                   c(     1,    2,    1,    2,    1),
                   c(     1,    1,    1,    2,    1),
                   c(     2,    2,    1,    1,    2),
                   c(     1,    1,    2,    1,    2),
                   c(     1,    1,    2,    2,    2),
                   c(     1,    2,    2,    2,    2),
                   c(     2,    2,    2,    1,    2),
                   c(     1,    1,    1,    1,    1),
                   c(     2,    1,    1,    1,    1),
                   c(     2,    1,    2,    1,    1),
                   c(     2,    2,    1,    1,    1),
                   c(     2,    2,    1,    2,    1),
                   c(     2,    2,    2,    1,    1))
    dimnames(haplo)[[2]] <- paste("loc", 1:ncol(haplo), sep=".")
    haplo <- data.frame(haplo)

    haplo.freq <- c(0.170020121, 0.162977867, 0.123742455, 0.117706237, 0.097585513, 0.084507042,
                    0.045271630, 0.039235412, 0.032193159, 0.019114688, 0.019114688, 0.013078471,
                    0.013078471, 0.013078471, 0.013078471, 0.006036217, 0.006036217, 0.006036217,
                    0.006036217, 0.006036217, 0.006036217)

    hPair <- get.hapPair(haplo, haplo.freq, base.index=1)
    names(hPair)
    dim(hPair$x.haplo)

[Package haplo.stats version 1.7.9 Index]