These functions remove gaps ("-") in a sample of DNA sequences.
del.gaps(x)
del.colgapsonly(x, threshold = 1, freq.only = FALSE)
del.rowgapsonly(x, threshold = 1, freq.only = FALSE)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.
a matrix, a list, or a vector containing the DNA or AA
sequences; only matrices for del.colgapsonly and for
del.rowgapsonly.
the largest gap proportion to delete the column or row.
if TRUE, returns only the numbers of gaps for
each column or row.
Emmanuel Paradis
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".
base.freq, seg.sites,
image.DNAbin, checkAlignment