searchGEO: Search GEO database

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

Search GEO database

Description

This function searches the 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 searchFieldsGEO.
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 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.frame contains the search results

See Also

searchFieldsGEO

Examples

## Not run: 
searchGEO("diabetes[ALL] AND Homo sapiens[ORGN] AND GSE[ETYP]")

## End(Not run)

seandavi/GEOquery documentation built on Oct. 29, 2024, 1:24 p.m.