seqinr (version 1.0-1)

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)
summary.SeqFastadna(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.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

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(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