bio_enrich {GWENA} | R Documentation

## 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)

[Package GWENA version 1.2.0 Index]