runEnrichment: Run enrichment analysis of a gene set for C. elegans

In oliviermfmartin/HelpingHand: A helping hand

Description

Wrapper function around enrichKEGG and enrichGO.

Usage

runEnrichment(
  gene,
  universe = NULL,
  keytype = "WORMBASE",
  pvalueCutoff = 1,
  use_internal_data = TRUE
)

Arguments

gene	a vector of entrez gene id.
universe	background genes. If missing, the all genes listed in the database (eg TERM2GENE table) will be used as background.
keytype	the keytype that matches the keys used. For the select methods, this is used to indicate the kind of ID being used with the keys argument. For the keys method this is used to indicate which kind of keys are desired from keys
pvalueCutoff	pvalue cutoff on enrichment tests to report
use_internal_data	logical, use KEGG.db or latest online KEGG data

Value

A list of enrichResult for KEGG and GO annotations.

oliviermfmartin/HelpingHand documentation built on Oct. 10, 2020, 5:59 a.m.