moduleDEA: Disease enrichment analysis of modules

In miRspongeR: Identification and analysis of miRNA sponge interaction networks and modules

Description

Disease enrichment analysis of modules. The disease ontology databases have three types including DO: Disease Ontology database (http://disease-ontology.org/), DGN: DisGeNET database (http://www.disgenet.org/), and NCG: Network of Cancer Genes database (http://ncg.kcl.ac.uk/).

Usage

moduleDEA(Modulelist, OrgDb = "org.Hs.eg.db", ont = "DO",
padjustvaluecutoff = 0.05, padjustedmethod = "BH")

Arguments

Modulelist	A list of miRNA sponge modules.
OrgDb	OrgDb
ont	One of "DO", and "DOLite" subontologies.
padjustvaluecutoff	A cutoff value of adjusted p-values.
padjustedmethod	Adjusted method of p-values, can select one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

Value

A list of disease enrichment analysis results.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)

References

Yu G, Wang L, Yan G, et al. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics, 2015, 31(4):608-609.

Examples

# Obtain miRNA-target interaction data file "miR2Target.csv" in csv format
miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR")
miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")
miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology")
spongenetwork_Cluster <- netModule(miRHomologyceRInt[, 1:2])
sponge_Module_DEA <- moduleDEA(spongenetwork_Cluster)

miRspongeR documentation built on Nov. 19, 2020, 2:01 a.m.