R: Access allele counts or frequencies

tab {adegenet} | R Documentation

## Access allele counts or frequencies

### Description

This accessor is used to retrieve a matrix of allele data. By default, a matrix of integers representing allele counts is returned. If `freq` is TRUE, then data are standardised as frequencies, so that for any individual and any locus the data sum to 1. The argument `NA.method` allows to replace missing data (NAs). This accessor replaces the previous function `truenames` as well as the function `makefreq`.

### Usage

    tab(x, ...)

    ## S4 method for signature 'genind'
    tab(x, freq = FALSE, NA.method = c("asis", "mean", "zero"), ...)

    ## S4 method for signature 'genpop'
    tab(x, freq = FALSE, NA.method = c("asis", "mean", "zero"), ...)

### Arguments

`x` | a genind or genpop object.
`...` | further arguments passed to other methods.
`freq` | a logical indicating if data should be transformed into relative frequencies (TRUE); defaults to FALSE.
`NA.method` | a method to replace NA; asis: leave NAs as is; mean: replace by the mean allele frequencies; zero: replace by zero

### Value

a matrix of integers or numeric

### Examples

    data(microbov)
    head(tab(microbov))
    head(tab(microbov,freq=TRUE))

[Package adegenet version 2.1.4 Index]