entrez_fetch: Download data from NCBI databases

Description

A set of unique identifiers mush be 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. See Table 1 in the linked reference for the set of formats available for each database.

Usage

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

Arguments

character, name of the database to use

vector (numeric or character), unique ID(s) for records in database db

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 'text'

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='xml'

References

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

Examples

Run this code

katipo <- "Latrodectus katipo[Organism]"
katipo_search <- entrez_search(db="nuccore", term=katipo)
kaitpo_seqs <- entrez_fetch(db="nuccore", id=katipo_search$ids, rettype="fasta")