bio3d: as.fasta – R documentation

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as.fasta

Alignment to FASTA object

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

as.fasta(x, id=NULL, ...)

`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.

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:

`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.

Lars Skjaerven

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

as.fasta(c("A", "C", "D"))

Biological Structure Analysis

v2.4-2

GPL (>= 2)

Authors

Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut]

Initial release