Effective number of genes

Count the number of genes in the Gesel database that belong to at least one set.

effectiveNumberOfGenes(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

Integer scalar specifying the number of genes in Gesel that belong to at least one set.

Details

The return value should be used as the total number of balls when performing a hypergeometric test for gene set enrichment (see phyper), instead of nrow(fetchAllGenes(species)). This ensures that uninteresting genes like pseudo-genes or predicted genes are ignored during the calculation. Otherwise, unknown genes would inappropriately increase the number of balls and understate the enrichment p-values.

Author

Aaron Lun