enrich_module: Enrichment analysis of each module

In jiang-junyao/IReNA: IReNA

Enrichment analysis of each module

Description

This function integrate clusterprofile make enrichment analysis for each moudle. Before run this function, you need to download the org.db for your species through BiocManager.

Usage

enrich_module(
  Kmeans_result,
  org.db,
  enrich.db,
  fun_num = 5,
  pvalueCutoff = 0.05,
  use_internal_data = TRUE,
  organism = NULL
)

Arguments

Kmeans_result	Kmeans result data.frame, row names should be ENSEMBEL ID, and the first column should be gene Symbol ID, the second column should be KmeansGroup
org.db	org.db of your species.
enrich.db	'GO' for GO enricment analysis, 'KEGG' for KEGG enrichment analysis
fun_num	numeric, indicating the number of output functions per module
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report
use_internal_data	logical, use KEGG.db or latest online KEGG data
organism	character, used for KEGG enrichment analysis. supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html'

Value

data.frame contains enrichment functions for each module

Examples

## Not run: 
library(org.Hs.eg.db)
Kmeans_cluster_Ens <- add_ENSID(clustering,Spec1='Hs')
enrichment <- enrich_module(Kmeans_cluster_Ens, org.Hs.eg.db, 'KEGG')
enrichment <- enrich_module(Kmeans_cluster_Ens, org.Hs.eg.db, 'GO')

## End(Not run)

jiang-junyao/IReNA documentation built on May 2, 2024, 6:54 a.m.