ape: del.gaps – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

ape

del.gaps

Delete Alignment Gaps in DNA Sequences

Description

These functions remove gaps ("-") in a sample of DNA sequences.

Usage

del.gaps(x)
del.colgapsonly(x, threshold = 1, freq.only = FALSE)
del.rowgapsonly(x, threshold = 1, freq.only = FALSE)

Arguments

`x`	a matrix, a list, or a vector containing the DNA sequences; only matrices for `del.colgapsonly` and for `del.rowgapsonly`.
`threshold`	the largest gap proportion to delete the column or row.
`freq.only`	if `TRUE`, returns only the numbers of gaps for each column or row.

Details

del.gaps remove all gaps, so the returned sequences may not have all the same lengths and are therefore returned in a list.

del.colgapsonly removes the columns with a proportion at least threshold of gaps. Thus by default, only the columns with gaps only are removed (useful when a small matrix is extracted from a large alignment). del.rowgapsonly does the same for the rows.

The sequences can be either in "DNAbin" or in another format, but the returned object is always of class "DNAbin".

Value

del.gaps returns a vector (if there is only one input sequence) or a list of class "DNAbin"; del.colgapsonly and del.rowgapsonly return a matrix of class "DNAbin" or a numeric vector (with names for the second function) if freq.only = TRUE.

Author(s)

Emmanuel Paradis

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