Fetch genes for all sets

Fetch the identities for genes in all sets in the Gesel database.

fetchGenesForAllSets(species, config = NULL)

Arguments

species

String containing the NCBI taxonomy ID of the species of interest.

config

Configuration list, typically created by newConfig. If NULL, the default configuration is used.

Value

List of integer vectors. Each vector represents a gene set, corresponding to the rows of the data frame returned by fetchAllSets. Each vector contains the identities of the genes in that set, where each integer is a gene index that refers to a row of the data frame returned by fetchAllGenes.

Author

Aaron Lun

Examples

all.sets <- fetchGenesForAllSets("9606")
length(all.sets)
#> [1] 40654

# Genes in the first set:
fetchAllGenes("9606")$symbol[all.sets[[1]]]
#> [[1]]
#> [1] "SLC25A4"
#> 
#> [[2]]
#> [1] "TYMP"
#> 
#> [[3]]
#> [1] "MEF2A"
#> 
#> [[4]]
#> [1] "MPV17"
#> 
#> [[5]]
#> [1] "OPA1"
#> 
#> [[6]]
#> [1] "LONP1"
#> 
#> [[7]]
#> [1] "AKT3"
#> 
#> [[8]]
#> [1] "SLC25A36"
#> 
#> [[9]]
#> [1] "PIF1"
#> 
#> [[10]]
#> [1] "SLC25A33"
#> 
#> [[11]]
#> [1] "MGME1"
#> 

# Details about the first set:
fetchAllSets("9606")[1,]
#>         name                      description size collection number
#> 1 GO:0000002 mitochondrial genome maintenance   11          1      1