R: Download data from NCBI databases

entrez_fetch {rentrez} | R Documentation

## Download data from NCBI databases

### Description

Pass unique identifiers to an NCBI database and receive data files in a variety of formats. A set of unique identifiers mustbe specified with either the `db` argument (which directly specifies the IDs as a numeric or character vector) or a `web_history` object as returned by `entrez_link`, `entrez_search` or `entrez_post`.

### Usage

    entrez_fetch(db, id = NULL, web_history = NULL, rettype, retmode = "",
      parsed = FALSE, config = NULL, ...)

### Arguments

`db` | character, name of the database to use
`id` | vector (numeric or character), unique ID(s) for records in database `db`. In the case of sequence databases these IDs can take form of an NCBI accession followed by a version number (eg AF123456.1 or AF123456.2).
`web_history,` | a web_history object
`rettype` | character, format in which to get data (eg, fasta, xml...)
`retmode` | character, mode in which to receive data, defaults to an empty string (corresponding to the default mode for rettype).
`parsed` | boolean should entrez_fetch attempt to parse the resulting file. Only works with xml records (including those with rettypes other than "xml") at present
`config` | vector, httr configuration options passed to httr::GET
`...` | character, additional terms to add to the request, see NCBI documentation linked to in references for a complete list

### Details

The format for returned records is set by that arguments `rettype` (for a particular format) and `retmode` for a general format (JSON, XML text etc). See Table 1 in the linked reference for the set of formats available for each database. In particular, note that sequence databases (nuccore, protein and their relatives) use specific format names (eg "native", "ipg") for different flavours of xml.

For the most part, this function returns a character vector containing the fetched records. For XML records (including 'native', 'ipg', 'gbc' sequence records), setting `parsed` to `TRUE` will return an `XMLInternalDocument`,

### Value

character string containing the file created

XMLInternalDocument a parsed XML document if parsed=TRUE and rettype is a flavour of XML.

### References

http://www.ncbi.nlm.nih.gov/books/NBK25499/#_chapter4_EFetch_

### See Also

`config` for available '`httr`' configs

### Examples

    ## Not run:
    katipo <- "Latrodectus katipo[Organism]"
    katipo_search <- entrez_search(db="nuccore", term=katipo)
    kaitpo_seqs <- entrez_fetch(db="nuccore", id=katipo_search$ids, rettype="fasta")
    #xml
    kaitpo_seqs <- entrez_fetch(db="nuccore", id=katipo_search$ids, rettype="native")

    ## End(Not run)

[Package rentrez version 1.2.1 Index]