seqinr (version 3.1-2)

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, name)
 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

name

the name of the sequence

Value

• as.SeqFrag returns a biological sequence 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 classfor sub-sequence
• is.SeqFrag returns TRUE if the object is of class Seqfrag.

References

citation("seqinr")

See Also

getFrag, getLength, getName, getSequence, getTrans

Examples

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