Alignment to FASTA object

Convert alignment/sequence in matrix/vector format to FASTA object.

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.

Details

This function provides basic functionality to convert a sequence character matrix/vector to a FASTA object.

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.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Author

Lars Skjaerven

See also

get.seq, seqaln, seqbind, pdbaln

Examples

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