R: AA sequence in Fasta Format

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)
    ## S3 method for class 'SeqFastaAA'
    summary(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

`citation("seqinr")`

### 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 3.4-5 Index]