del.gaps {ape}

Delete Alignment Gaps in DNA or AA 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 or AA 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 class of the input sequences is respected and kept unchanged, unless it contains neither "DNAbin" nor "AAbin" in which case the object is first converted into the class "DNAbin".

Value

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

Author(s)

Emmanuel Paradis

See Also

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