tab: Access allele counts or frequencies

In adegenet: Exploratory Analysis of Genetic and Genomic Data

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))

adegenet documentation built on Feb. 16, 2023, 6 p.m.