Convert alignment/sequence in matrix/vector format to FASTA object.
Usage
as.fasta(x, id=NULL, ...)
Arguments
x
a sequence character matrix/vector (e.g obtained from
get.seq or seqbind).
id
a vector of sequence names to serve as sequence
identifers. By default the function will use the row names of the
alignment if they exists, otherwise ids will be generated.
...
arguments passed to and from functions.
Value
Returns a list of class "fasta" with the following components:
ali
an alignment character matrix with a row per sequence and
a column per equivalent aminoacid/nucleotide.
id
sequence names as identifers.
call
the matched call.
Details
This function provides basic functionality to convert a sequence
character matrix/vector to a FASTA object.
References
Grant, B.J. et al. (2006) Bioinformatics22, 2695--2696.