Fetch sets for some genes — fetchSetsForSomeGenes • gesel

Fetch all sets that contain some genes in the Gesel database. This can be more efficient than fetchSetsForAllGenes if only a few genes are of interest.

fetchSetsForSomeGenes(species, genes, config = NULL)

Arguments

species: String containing the NCBI taxonomy ID of the species of interest.
genes: Integer vector containing gene indices. Each gene index refers to a row of the data frame returned by fetchAllGenes).
config: Configuration list, typically created by newConfig. If NULL, the default configuration is used.

Value

List of integer vectors. Each vector corresponds to a gene in genes and contains the identities of the sets containing that gene. Each set is defined by its set index, which refers to a row of the data frame returned by fetchAllSets.

Author

Aaron Lun

Examples

first.gene <- fetchSetsForSomeGenes("9606", 1)
str(first.gene)
#> List of 1
#>  $ : int [1:68] 1327 2337 2366 3538 6639 8166 13182 13273 14384 17635 ...

# Sets containing the first gene
all.set.info <- fetchAllSets("9606")
head(all.set.info[first.gene[[1]],])
#>            name                  description size collection number
#> 1327 GO:0003674           molecular_function  710          1   1327
#> 2337 GO:0005576         extracellular region 1916          1   2337
#> 2366 GO:0005615          extracellular space 1865          1   2366
#> 3538 GO:0008150           biological_process  561          1   3538
#> 6639 GO:0031093 platelet alpha granule lumen   67          1   6639
#> 8166 GO:0034774      secretory granule lumen  115          1   8166