R: Base frequencies from DNA Sequences

base.freq {ape} | R Documentation

## Base frequencies from DNA Sequences

### Description

`base.freq` computes the frequencies (absolute or relative) of the four DNA bases (adenine, cytosine, guanine, and thymidine) from a sample of sequences.

`GC.content` computes the proportion of G+C (using the previous function). All missing or unknown sites are ignored.

`Ftab` computes the contingency table with the absolute frequencies of the DNA bases from a pair of sequences.

### Usage

    base.freq(x, freq = FALSE, all = FALSE)
    GC.content(x)
    Ftab(x, y = NULL)

### Arguments

`x` | a vector, a matrix, or a list which contains the DNA sequences.
`y` | a vector with a single DNA sequence.
`freq` | a logical specifying whether to return the proportions (the default) or the absolute frequencies (counts).
`all` | a logical; by default only the counts of A, C, G, and T are returned. If `all = TRUE`, all counts of bases, ambiguous codes, missing data, and alignment gaps are returned.

### Details

The base frequencies are computed over all sequences in the sample.

For `Ftab`, if the argument `y` is given then both `x` and `y` are coerced as vectors and must be of equal length. If `y` is not given, `x` must be a matrix or a list and only the two first sequences are used.

### Value

A numeric vector with names `c("a", "c", "g", "t")` (and possibly `"r", "m", ...`, a single numeric value, or a four by four matrix with similar dimnames.

### Author(s)

Emmanuel Paradis

### See Also

`seg.sites`, `nuc.div`, `DNAbin`

### Examples

    data(woodmouse)
    base.freq(woodmouse)
    base.freq(woodmouse, TRUE)
    base.freq(woodmouse, TRUE, TRUE)
    GC.content(woodmouse)
    Ftab(woodmouse)
    Ftab(woodmouse[1, ], woodmouse[2, ]) # same than above
    Ftab(woodmouse[14:15, ]) # between the last two

[Package ape version 4.1 Index]