Generic function to extract sequence fragments
getFrag is used to extract the sequence fragment starting at the begin position
and ending at the end position.
getFrag(object, begin, end, ...) ## S3 method for class 'SeqAcnucWeb' getFrag(object, begin, end, ..., socket = autosocket(), name = getName(object)) ## S3 method for class 'SeqFastadna' getFrag(object, begin, end, ..., name = getName(object)) ## S3 method for class 'SeqFastaAA' getFrag(object, begin, end, ..., name = getName(object)) ## S3 method for class 'SeqFrag' getFrag(object, begin, end, ..., name = getName(object))
object |
an object of the class |
begin |
First position of the fragment to extract. This position is included. Numerotation starts at 1. |
end |
Last position of the fragment to extract. This position is included. |
socket |
an object of class |
name |
the sequence name |
... |
further arguments passed to or from other methods |
getFrag returns an object of class SeqFrag.
D. Charif, J.R. Lobry, L. Palmeira
citation("seqinr")
#
# List all available methods for getFrag generic function:
#
methods(getFrag)
#
# Example with a DNA sequence from a FASTA file:
#
dnafile <- system.file("sequences/malM.fasta", package = "seqinr")
sfdna <- read.fasta(file = dnafile)
myfrag <- getFrag(sfdna[[1]], begin = 1, end = 10)
stopifnot(getSequence(myfrag, as.string = TRUE) == "atgaaaatga")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.