bio_enrich: Modules enrichment

In Kumquatum/GWENA: Pipeline for augmented co-expression analysis

Modules enrichment

Description

Enrich genes list from modules.

Usage

bio_enrich(module, custom_gmt = NULL, ...)

Arguments

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.

Value

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.

Examples

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)

Kumquatum/GWENA documentation built on July 7, 2023, 3:41 p.m.