R: Haplotype Frequencies With a Covariate

haploFreq {pegas} | R Documentation

## Haplotype Frequencies With a Covariate

### Description

This utility function extracts the absolute frequencies of haplotypes with respect to a categorical variable (a factor). The output is useful when ploting haplotype networks.

### Usage

    haploFreq(x, fac, split = "_", what = 2, haplo = NULL)

### Arguments

`x` | a set of DNA sequences (as an object of class `"DNAbin"`).
`fac` | a factor giving the categorical variable (can be missing).
`split` | a single character (see details).
`what` | a single integer (see details).
`haplo` | an object of class `"haplotype"`.

### Details

The frequencies of each haplotype in `x` are counted with respect to a factor which is either specified with `fac`, or extracted from the labels of `x`. In the second case, these labels are split with respect to the character specified in `split` and the `what`'th substrings are extracted and taken as the categorical variable (see example).

If `haplo` is specified, the haplotype frequencies are taken from it, otherwise they are calculated from `x`.

### Value

a matrix of counts.

### Author(s)

Klaus Schliep and Emmanuel Paradis

### See Also

`haplotype`, `haploNet`

### Examples

    ## generate some artificial data from 'woodmouse':
    data(woodmouse)
    x <- woodmouse[sample(15, size = 50, replace = TRUE), ]
    ## labels IdXXX_PopXXX_LocXXX
    rownames(x) <- paste("Id", 1:50, "_Pop", 1:2, "_Loc", 1:5, sep = "")
    head(labels(x))
    h <- haplotype(x)
    ## frequencies of haplotypes wrt 'Pop':
    f.pop <- haploFreq(x, haplo = h)
    ## frequencies of haplotypes wrt 'Loc':
    f.loc <- haploFreq(x, what = 3, haplo = h)
    nt <- haploNet(h)
    fq <- attr(nt, "freq")
    op <- par(mfcol = c(1, 2))
    plot(nt, size = fq, pie = f.pop, labels = FALSE)
    plot(nt, size = fq, pie = f.loc, labels = FALSE)
    par(op)

[Package pegas version 0.13 Index]