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
Value
character string containing the file created
XMLInternalDocument a parsed XML document if parsed=TRUE and rettype is a flavour of XML.
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,
See also
config for available 'httr` configs
Examples
if (FALSE) { # \dontrun{
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")
} # }