genbank {annotate} | R Documentation

## A function to open the browser to Genbank with the selected gene.

### Description

Given a vector of Genbank accession numbers or NCBI UIDs, the user can either have a browser display a URL showing a Genbank query for those identifiers, or a XMLdoc object with the same data.

### Usage

    genbank(...,disp=c("data","browser"), type=c("accession","uid"),
            pmaddress=.pmfetch("Nucleotide", disp, type))

### Arguments

`...` | Vectorized set of Genbank accession numbers or NCBI UIDs
`disp` | Either "Data" or "Browser" (default is data). Data returns a XMLDoc, while Browser will display information in the user's browser.
`type` | Denotes whether the arguments are accession numbers or UIDS. Defaults to accession values.
`pmaddress` | Specific path to the pubmed pmfetch engine from the NCBI website.

### Details

A simple function to retrieve Genbank data given a specific ID, either through XML or through a web browser. This function will accept either Genbank accession numbers or NCBI UIDs (defined as a Pubmed ID or a Medline ID) - although the types must not be mixed in a single call.

WARNING: The powers that be at NCBI have been known to ban the IP addresses of users who abuse their servers (currently defined as less then 2 seconds between queries). Do NOT put this function in a tight loop or you may find your access revoked.

### Value

If the option "data" is used, an object of type XMLDoc is returned, unless there was an error with the query in which case an object of type try-error is returned.
If the option "browser" is used, nothing is returned.

### Author(s)

R. Gentleman

### See Also

`pubmed`, `locuslinkByID`, `locuslinkQuery`, `xmlTreeParse`

### Examples

       ## Use UIDs to get data in both browser & data forms

       if ( interactive() ) {
          disp <- c("data","browser")
       } else {
          disp <- "data"
       }

       for (dp in disp)
         genbank("12345","9997",disp=dp,type="uid")

       ## Use accession numbers to retrieve browser info
       if ( interactive() )
           genbank("U03397","AF030427",disp="browser")

[Package annotate version 1.12.1 Index]