del.gaps
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.colgapsonlyand fordel.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.