bio_enrich {GWENA} | R Documentation |
Enrich genes list from modules.
bio_enrich(module, custom_gmt = NULL, ...)
module |
vector or list, vector of gene names representing a module or a named list of this modules. |
custom_gmt |
string or list, path to a gmt file or a list of these path. |
... |
any other parameter you can provide to gprofiler2::gost function. |
A gprofiler2::gost output, meaning a named list containing a 'result' data.frame with enrichement information on the differents databases and custom gmt files, and a 'meta' list containing informations on the input args, the version of gost, timestamp, etc. For more detail, see ?gprofiler2::gost.
custom_path <- system.file("extdata", "h.all.v6.2.symbols.gmt", package = "GWENA", mustWork = TRUE) single_module <- c("BIRC3", "PMAIP1", "CASP8", "JUN", "BCL2L11", "MCL1", "IL1B", "SPTAN1", "DIABLO", "BAX", "BIK", "IL1A", "BID", "CDKN1A", "GADD45A") single_module_enriched <- bio_enrich(single_module, custom_path) multi_module <- list(mod1 = single_module, mod2 = c("TAF1C", "TARBP2", "POLH", "CETN2", "POLD1", "CANT1", "PDE4B", "DGCR8", "RAD51", "SURF1", "PNP", "ADA", "NME3", "GTF3C5", "NT5C")) multi_module_enriched <- bio_enrich(multi_module, custom_path)