del.gaps

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Delete Alignment Gaps in DNA Sequences

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

Keywords
univar
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.

See Also

base.freq, seg.sites, image.DNAbin, checkAlignment

Aliases
  • del.gaps
  • del.colgapsonly
  • del.rowgapsonly
Documentation reproduced from package ape, version 5.3, License: GPL (>= 2)

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