seqinr (version 1.0-6)

SeqFrag: 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.

References

� citation("seqinr")

See Also

getFrag

Examples

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