# base.freq

From ape v2.6-3
0th

Percentile

##### Base frequencies from DNA Sequences

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

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

Keywords
manip, univar
##### Usage
base.freq(x, freq = FALSE)
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).
##### Details

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

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"), or a four by four matrix with similar dimnames.

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

• base.freq
• Ftab
##### Examples
data(woodmouse)
base.freq(woodmouse)
base.freq(woodmouse, TRUE)
Ftab(woodmouse)
Ftab(woodmouse[1, ], woodmouse[2, ]) # same than above
Ftab(woodmouse[14:15, ]) # between the last two
Documentation reproduced from package ape, version 2.6-3, License: GPL (>= 2)

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