Convert alignment/sequence in matrix/vector format to FASTA object.
as.fasta(x, id=NULL, ...)
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.
This function provides basic functionality to convert a sequence character matrix/vector to a FASTA object.
Returns a list of class
"fasta" with the following components:
an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide.
sequence names as identifers.
the matched call.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
as.fasta(c("A", "C", "D"))#> 1 3 #> seq1 ACD #> 1 3 #> #> Call: #> as.fasta(x = c("A", "C", "D")) #> #> Class: #> fasta #> #> Alignment dimensions: #> 1 sequence rows; 3 position columns (3 non-gap, 0 gap) #> #> + attr: id, ali, call