R: Class for DNA sequence in Fasta Format

SeqFastadna {seqinr} | R Documentation

## Class for DNA sequence in Fasta Format

### Description

`as.SeqFastadna` is called by many functions as `read.fasta`. It creates an object of class `SeqFastadna`. `is.SeqFastadna` returns TRUE if the object is of class `SeqFastadna`. `summary.SeqFastadna` gives the base composition of an object of class `SeqFastadna`.

### Usage

    as.SeqFastadna(object, name = NULL, Annot = NULL)
    is.SeqFastadna(object)
    ## S3 method for class 'SeqFastadna'
    summary(object, alphabet = s2c("acgt"), ...)

### 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
`alphabet` | a vector of single characters

### Value

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

`length` | the legth of the sequence
`compo` | the base counting of the sequence
`GC` | the percentage of G+C in the sequence

### Author(s)

D. Charif

### References

`citation("seqinr")`

### Examples

     s <- read.fasta(system.file("sequences/malM.fasta",package="seqinr"))
     is.SeqFastadna(s[[1]])
     summary(s[[1]])
     myseq <- s2c("acgttgatgctagctagcatcgat")
     as.SeqFastadna(myseq, name = "myseq", Annot = "blablabla")
     myseq

[Package seqinr version 3.4-5 Index]