find_public_datasets: find_public_datasets

In reactome/ReactomeGSA: Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

find_public_datasets

Description

Search for a public dataset in the resources supported by ReactomeGSA as external data sources.

Usage

find_public_datasets(
  search_term,
  species = "Homo sapiens",
  reactome_url = NULL
)

Arguments

search_term	The search terms as a single string. Multiple words (seperated by a space) are combined by an "AND".
species	Limit the search to selected species. The complete list of available species can be retrieved through get_public_species. By default, entries as limited to human datasets.
reactome_url	URL of the Reactome API Server. Overwrites the URL set in the 'reactome_gsa.url' option. Specific ports can be set using the standard URL specification (for example http://your.service:1234)

Value

A data.frame containing a list of datasets found through the search.

Examples

# search for any public dataset relating to BRAF in melanoma
melanoma_datasets <- find_public_datasets("melanoma braf")

# it is also possible to limit this to another species than human
melanoma_mouse <- find_public_datasets("melanoma", species = "Mus musculus")

# the list of available species can be retrieved using get_public_species
all_species <- get_public_species()

# datasets can then be loaded using the load_public_dataset function

reactome/ReactomeGSA documentation built on Nov. 9, 2024, 10:56 a.m.