searchGEO: Search GEO database

In seandavi/GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)

Search GEO database

Description

This function searchs [GDS](https://www.ncbi.nlm.nih.gov/gds) database, and return a data.frame for all the search results.

Usage

searchGEO(query, step = 500L)

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][rentrez::entrez_db_searchable].

step

the number of records to fetch from the database each time. You may choose a smaller value if failed.

Details

The NCBI allows users to access more records (10 per second) if they register for and use an API key. [set_entrez_key][rentrez::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][base::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.frame contains the search results

Examples

GEOquery::searchGEO("diabetes[ALL] AND Homo sapiens[ORGN] AND GSE[ETYP]")

seandavi/GEOquery documentation built on July 18, 2023, 4:30 p.m.