| deleteGaps {ips} | R Documentation |
Remove Gap Positions From DNA Sequences
Description
Remove indel positions (or gaps) from a DNA sequence
alignment. For faster execution, deleteGaps handles sequences
in ape's bit-level coding scheme.
Usage
deleteGaps(x, gap.max = nrow(x) - 4)
Arguments
x |
An object of class |
gap.max |
An integer, which gives the maximum number of
gap characters ("-") that will be tolerated at any given alignment
position (column). Only values between |
Details
The default, nmax = nrow(x) - 4, removes all those
positions from the alignment, which contain at least four non-gap
characters, which is the minimum number of sequences needed to
produce a non-trivial unrooted topology. All gaps will be excluded
by selecting nmax = 0 and half of all gaps with nmax =
nrow(x) / 2.
In contrast, del.gaps removes all gap characters
from the alignment, so most probably the result will not be a set of
sequences of equal length and the matrix will be coerced to a list.
Value
An object of class DNAbin.
See Also
code.simple.gaps for coding of simple gaps,
del.gaps for removal of all gap symbols from an
alignment, gblocks and aliscore for more
sophisticated methods of cleaning/masking alignments.