SeqFrag: Class for sub-sequences

In seqinr: Biological Sequences Retrieval and Analysis

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.

Author(s)

D. Charif, J.R. Lobry

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) 	

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