Search set text — searchSetText • gesel

Search for sets based on their names and descriptions.

searchSetText(
  species,
  query,
  use.name = TRUE,
  use.description = TRUE,
  config = NULL
)

Arguments

species: String containing the NCBI taxonomy ID of the species of interest.
query: String containing one or more words to search on. A set is only matched if it matches to all of the tokens in the query. The * and ? wildcards can be used to match to any or one character, respectively.
use.name: Logical scalar indicating whether to search on the name of the set.
use.description: Logical scalar indicating whether to search on the description of the set.
config: Configuration list, typically created by newConfig. If NULL, the default configuration is used.

Value

Integer vector of set indices for the matching gene sets. Each set index refers to a row in the data frame returned by fetchAllSets.

Author

Aaron Lun

Examples

out <- searchSetText("9606", "cancer")
fetchSomeSets("9606", out[1])
#>                            name
#> 1 SOGA_COLORECTAL_CANCER_MYC_DN
#>                                                                          description
#> 1 http://www.gsea-msigdb.org/gsea/msigdb/human/geneset/SOGA_COLORECTAL_CANCER_MYC_DN
#>   size collection number
#> 1   71          3      2

out <- searchSetText("9606", "innate immun*")
fetchSomeSets("9606", out[1])
#>                            name
#> 1 REACTOME_INNATE_IMMUNE_SYSTEM
#>                                                                          description
#> 1 http://www.gsea-msigdb.org/gsea/msigdb/human/geneset/REACTOME_INNATE_IMMUNE_SYSTEM
#>   size collection number
#> 1 1118          5    230