SeqFrag {seqinr}R Documentation

Class for sub-sequences

Description

as.SeqFrag is called by all methods of getFrag, but not directly by the users. It creates an object sequence of class SeqFrag.

Usage

 as.SeqFrag(object, begin, end, compl = FALSE, name = "frag")
 is.SeqFrag(object)

Arguments

object an object sequence of class seqFastadna, seqFastaAA, seqAcnucWeb or seqFrag
begin the first base of the fragment to get
end the last base of the fragment to get
compl if TRUE, you must give a name for the sequence
name the name of the fragment of the sequence

Value

as.SeqFrag returns a biological sequence representing by a vector of chars with the following attributes:

seqMother the name of the sequence from which the sequence comes
begin the position of the first base of the fragment on the mother sequence
end the position of the last base of the fragment on the mother sequence
class SeqFrag which is the newest class of the sequence

is.SeqFrag returns TRUE if the object is of class Seqfrag.

Author(s)

D. Charif

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.

See Also

getFrag

Examples

 s = read.fasta(File=system.file("sequences/malM.fasta",package = "seqinr"))
 getFrag(s[[1]],1,10)   

[Package seqinr version 1.0-2 Index]