SeqFastadna: Class for DNA sequence in Fasta Format

In seqinr: Biological Sequences Retrieval and Analysis

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

seqinr documentation built on May 29, 2024, 6:36 a.m.