format_DO: Reformat a Disease Ontology database.

In keita-iida/ASURATDB: ASURAT database builder

Reformat a Disease Ontology database.

Description

This function reformats a Disease Ontology database.

Usage

format_DO(dict = NULL, all_geneIDs = NULL, orgdb = NULL)

Arguments

dict	A res slot of enrichDO().
all_geneIDs	All genes in the form of ENTREZ ID.
orgdb	A genome annotation package.

Value

A formatted database.

Examples

## Not run: 
# Below may be time-consuming runs.
library(DOSE)
data(DO2EG)
dict_DO <- enrichDO(unlist(DO2EG), ont = "DO", pvalueCutoff = 1,
                    pAdjustMethod = "BH", minGSSize = 0, maxGSSize = 1e+10,
                    qvalueCutoff = 1, readable = FALSE)
human_DO <- format_DO(dict = dict_DO@result, all_geneIDs = dict_DO@gene,
                      orgdb = org.Hs.eg.db::org.Hs.eg.db)

## End(Not run)

keita-iida/ASURATDB documentation built on Feb. 21, 2023, 6:05 p.m.