gapless_msa {orthGS} | R Documentation |
Remove Gaps in a MSA
Description
Removes gaps in a given msa.
Usage
gapless_msa(msa, seqtype = 'AA', df = TRUE, sfile = FALSE)
Arguments
msa |
input alignment. |
seqtype |
the nature of the sequences: 'DNA' or 'AA'. |
df |
logical. When TRUE msa should be a matrix, when FALSE msa should be a string giving the path to a fasta file containing the alignment. |
sfile |
if different to FALSE, then it should be a string indicating the path to save a fasta alignment file. |
Details
It should be noted that this function does not carry out the alignment itself.
Value
an alignment without gaps in form of matrix or a file containing such an alignment in fasta format.
See Also
msa
Examples
# Example 1:
aln <- matrix(c("A", "P", "G", "W", "-", "-",
"-", "A", "G", "W", "C", "-",
"-", "-", "C", "W", "G", "A" ), nrow = 3, byrow =TRUE)
gapless_msa(aln)
# Example 2:
## Not run: gapless_msa(msa(sequences = c("APGW", "AGWC", "CWGA"),
ids = c("a", "b", "c"))$ali)
## End(Not run)
[Package orthGS version 0.1.6 Index]