keyword_enrichment_from_GO: Keyword enrichment for GO terms

In jokergoo/simplifyEnrichment: Simplify Functional Enrichment Results

Keyword enrichment for GO terms

Description

Keyword enrichment for GO terms

Usage

keyword_enrichment_from_GO(go_id, min_bg = 5, min_term = 2)

Arguments

go_id	A vector of GO IDs.
min_bg	Minimal number of GO terms (in the background, i.e. all GO temrs in the GO database) that contain a specific keyword.
min_term	Minimal number of GO terms (GO terms in go_id) that contain a specific keyword.

Details

The enrichment is applied by Fisher's exact test. For a keyword, there is the following 2x2 contigency table:

                      | contains the keyword | does not contain the keyword
    In the GO set     |          s11         |          s12
    Not in the GO set |          s21         |          s22

where s11, s12, s21 and s22 are the counts of GO terms in the four categories.

Value

A data frame with keyword enrichment results.

Examples

go_id = random_GO(100)
keyword_enrichment_from_GO(go_id)

jokergoo/simplifyEnrichment documentation built on Sept. 16, 2024, 8:39 a.m.