ape: base.freq – R documentation

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base.freq

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

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

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24