R: Print and Summaries of Loci Objects

summary.loci {pegas} | R Documentation

## Print and Summaries of Loci Objects

### Description

These functions print and summarize table of alleles and loci (objects of class `"loci"`).

### Usage

    ## S3 method for class 'loci'
    print(x, details = FALSE, ...)
    ## S3 method for class 'loci'
    summary(object, ...)
    ## S3 method for class 'summary.loci'
    print(x, ...)
    ## S3 method for class 'loci'
    x[i, j, drop = FALSE]
    ## S3 method for class 'summary.loci'
    plot(x, loci, what = "both", layout = 1, col = c("blue", "red"), ...)

### Arguments

`x, object` | an object of class `"loci"` or `"summary.loci"`.
`details` | a logical value: if `TRUE` the data are printed as a data frame; the default is `FALSE`.
`i, j` | indices of the rows and/or columns to select or to drop. They may be numeric, logical, or character (in the same way than for standard R objects).
`drop` | a logical specifying whether to returned an object of the smallest dimension possible, i.e., may return a vector or a factor if `drop = TRUE` (this is not the default).
`loci` | the loci (genes) to be plotted. By default, all loci are plotted.
`what` | the frequencies to be plotted. Three choices are possible: `"alleles"`, `"genotypes"`, and `"both"` (the default), or any unambiguous abbreviations.
`layout` | the number of graphs to be plotted simultaneously.
`col` | the colours used for the barplots.
`...` | further arguments to be passed to or from other methods.

### Details

Genotypes not observed in the data frame are not counted.

When using the `[` method, if only one column is extracted and the option `drop = TRUE`, or if the returned data frame has no ‘locus’ column, then the class `"loci"` is dropped. The option `drop = FALSE` (default) keeps the class (see examples).

An object of class `"loci"` can be edited in the R data editor with, e.g., `fix(x)` or `x <- edit(x)`.

`summary.loci` computes the absolute frequencies (counts); see the examples on how to compute the relative frequencies (proportions).

### Value

`summary.loci` returns a list with the genes as names and each element made a list with two vectors `"genotype"` and `"allele"` with the frequencies (numbers) of genotypes and alleles, respectively. The names of these two vectors are the observed genotypes and alleles.

`print` and `plot` methods return NULL.

### Author(s)

Emmanuel Paradis

### See Also

`read.loci`, `getAlleles`, `edit.loci`

### Examples

    data(jaguar)
    s <- summary(jaguar)
    ## Not run:
    ## works if the device is large enough:
    plot(s, layout = 30, las = 2)
    layout(1)

    ## End(Not run)
    ## compute the relative frequencies:
    rapply(s, function(x) x/sum(x), how = "replace")
    ## extract a single locus:
    jaguar[, 1]
    jaguar[, 1, drop = TRUE] # returns a vector
    jaguar[[1]]              # also returns a vector

[Package pegas version 1.1 Index]