getLocation: Generic function to get the location of subsequences on the...

In seqinr: Biological Sequences Retrieval and Analysis

Generic function to get the location of subsequences on the parent sequence

Description

This function works only with subsequences from an ACNUC server.

Usage

getLocation(object, ...)
## S3 method for class 'SeqAcnucWeb'
getLocation(object, ..., socket = autosocket())

Arguments

object	an object of the class SeqAcnucWeb, or a list of them, or an object created by query
socket	an object of class sockconn connecting to a remote ACNUC database (default is a socket to the last opened database by choosebank).
...	further arguments passed to or from other methods

Value

A list giving the positions of the sequence on the parent sequence. If the sequence is a subsequence (e.g. coding sequence), the function returns the position of each exon on the parent sequence. NA is returned for parent sequences and a warning is isued.

Author(s)

D. Charif, J.R. Lobry, L. Palmeira

References

citation("seqinr")

See Also

SeqAcnucWeb

Examples

#
# List all available methods for getLocation generic function:
#
   methods(getLocation)
#
# Example with a subsequence from an ACNUC server:
#
  ## Not run: 
  # Need internet connection
  choosebank("emblTP")
  fc <- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
  getLocation(fc$req[[5]])
  closebank()  

## End(Not run)

seqinr documentation built on March 31, 2023, 3:05 p.m.