read.fasta {seqinr}R Documentation

Read file in fasta format

Description

Read a file containing sequences in fasta format.

Usage

read.fasta(File = system.file("sequences/ct.fasta", package = "seqinr"),seqtype="DNA")

Arguments

File The name of the file which the sequences in fasta format are to be read from. If it does not contain an absolute path, the file name is relative to the current working directory, getwd()
seqtype the nature of the sequence: DNA or AA

Details

By default read.fasta

Value

return a list of vector of chars. Each element is a sequence object of the class SeqFastadna or SeqFastaAA.

Author(s)

D. Charif

References

  To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.

Examples

s = read.fasta(File=system.file("sequences/malM.fasta",package = "seqinr"))
ss = read.fasta(File=system.file("sequences/seqAA.fasta",package = "seqinr"),seqtype="AA")

[Package seqinr version 1.0-3 Index]