module_compare: Compare enrichment by modules

In MahShaaban/rkip: Gene co-expression analysis of RKIP, autophagy and EMT in prostate cancer

Description

Awrapper to run comparCluster, gofiler and extract results

Usage

module_compare(index, level = 4, ...)

Arguments

index	A list of items each is a set og gene IDs
level	An integer, the Gene Ontology
...	Other arguments passed to compareCluster

Value

A data.frame as in the slot compareClusterResult

Examples

## Not run: 
# load required libraries
library(org.Mm.eg.db)

# make an index of gene sets
ind <- list(blue = c("Acbd5", "Atg5", "Atm", "Bmf"),
            brown = c("Atg4c", "Il3", "Lamp3", "Lepr", "Mefv"))

# run comparison
module_compare(ind,
               fun = 'enrichGO',
               OrgDb = org.Mm.eg.db,
               keyType = 'SYMBOL',
               ont = 'MF',
               pAdjustMethod = 'fdr')

## End(Not run)

MahShaaban/rkip documentation built on May 23, 2019, 8:37 a.m.