base.freq {ape}R Documentation

Base frequencies from DNA Sequences

Description

This function computes the relative frequencies (i.e. percentages) of the four DNA bases (adenine, cytosine, guanine, and thymidine) from a sample of sequences.

Usage

base.freq(x)

Arguments

x a vector, a matrix, or a list which contains the DNA sequences.

Details

The base frequencies are computed over all sequences in the sample. All missing or unknown sites are discarded from the computations.

Value

A numeric vector stoting the relative frequencies with names c("a", "c", "g", "t").

Author(s)

Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr

See Also

GC.content, seg.sites, nuc.div, DNAbin


[Package ape version 2.3 Index]