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Search GEO database

Source: R/searchGEO.R
searchGEO.Rd

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.

Value

a data.frame contains the search results

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

See also

searchFieldsGEO

Examples

if (FALSE) { # \dontrun{
searchGEO("diabetes[ALL] AND Homo sapiens[ORGN] AND GSE[ETYP]")
} # }