SeqFastaAA {seqinr}R Documentation

AA sequence in Fasta Format

Description

as.SeqFastaAA is called by the function as read.fasta. It creates an object of class SeqFastaAA. is.SeqFastaAA returns TRUE if the object is of class SeqFastaAA. summary.SeqFastaAA gives the AA composition of an object of class SeqFastaAA.

Usage

as.SeqFastaAA(object, name = NULL, Annot = NULL)
is.SeqFastaAA(object)
summary.SeqFastaAA(object,...)

Arguments

object a vector of chars representing a biological sequence
name NULL a character string specifying a name for the sequence
Annot NULL a character string specifying some annotations for the sequence
... additional arguments affecting the summary produced

Value

as.SeqFastaAA returns an object sequence of class SeqFastaAA. summary.SeqFastaAA returns a list which the following components:

composition the AA counting of the sequence
AA.Property the percentage of each group of amino acid in the sequence. By example, the groups are small, tiny, aliphatic, aromatic ...

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/seqAA.fasta",package="seqinr"),seqtype="AA")
  is.SeqFastaAA(s[[1]])
  summary(s[[1]])
  myseq = s2c("MSPTAYRRGSPAFLV*")
  as.SeqFastaAA(myseq, name = "myseq", Annot = "blablabla")
  myseq
[Package seqinr version 1.0-2 Index]