search_geo: Search GEO database

In Yunuuuu/rgeo: R interface for GEO database

Search GEO database

Description

This function searchs GDS database, and return a data.frame for all the search results.

Usage

search_geo(query, step = 500L, interval = 1L)

Arguments

query	character, the search term. The NCBI uses a search term syntax which can be associated with a specific search field with square brackets. So, for instance "Homo sapiens[ORGN]" denotes a search for ⁠Homo sapiens⁠ in the “Organism” field. Details see https://www.ncbi.nlm.nih.gov/geo/info/qqtutorial.html. The names and definitions of these fields can be identified using entrez_db_searchable.
step	the number of records to fetch from the database each time. You may choose a smaller value if failed.
interval	The time interval (seconds) between each step.

Details

The NCBI allows users to access more records (10 per second) if they register for and use an API key. set_entrez_key function allows users to set this key for all calls to rentrez functions during a particular R session. You can also set an environment variable ENTREZ_KEY by Sys.setenv. Once this value is set to your key rentrez will use it for all requests to the NCBI. Details see https://docs.ropensci.org/rentrez/articles/rentrez_tutorial.html#rate-limiting-and-api-keys

Value

A data.table contains the search results

Examples

  rgeo::search_geo("diabetes[ALL] AND Homo sapiens[ORGN] AND GSE[ETYP]")

Yunuuuu/rgeo documentation built on Dec. 23, 2024, 10:01 p.m.