rentrez (version 0.3.1)

entrez_search: Search the NCBI databases using EUtils

Description

Contstructs a query with the given arguments, including a search term, and a darabase name, then retrieves the XML document created by that query. See package-level documentation for general advice on using the Entrez functions

Usage

entrez_search(db, term, config = NULL, ...)

Arguments

db

character Name of the database to search for

term

character The search term

...

character Additional terms to add to the request

config

vector configuration options passed to httr::GET

Value

• ids integer Unique IDS returned by the search

  count integer Total number of hits for the search

  retmax integer Maximum number of hits returned by the search

  QueryKey integer identifier for specific query in webhistory

  WebEnv character identifier for session key to use with history

  file XMLInternalDocument xml file resulting from search, parsed with xmlTreeParse

See Also

config for avaliable configs

Examples

query <- "Gastropoda[Organism] AND COI[Gene]"
   web_env_search <- entrez_search(db="nuccore", query, usehistory="y")
   cookie <- web_env_search$WebEnv
   qk <- web_env_search$QueryKey
   snail_coi <- entrez_fetch(db = "nuccore", WebEnv = cookie, query_key = qk,
                             file_format = "fasta", retmax = 10)