seqinr (version 4.2-36)

SeqFastadna: 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 SeqFastadna
summary(object, alphabet = s2c("acgt"), ...)

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

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

Author

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