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

getLocation {seqinr} | R Documentation

## 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)

[Package seqinr version 3.4-5 Index]