moduleFEA: Functional GO, KEGG and Reactome enrichment analysis of...

In zhangjunpeng411/miRsponge: Identification and analysis of miRNA sponge regulation

Functional GO, KEGG and Reactome enrichment analysis of modules

Description

Functional GO, KEGG and Reactome enrichment analysis of modules. GO: Gene Ontology database (http://www.geneontology.org/), KEGG: Kyoto Encyclopedia of Genes and Genomes Pathway Database (http://www.genome.jp/kegg/) and Reactome: Reactome Pathway Database (http://reactome.org/).

Usage

moduleFEA(Modulelist, ont = "BP", KEGGorganism = "hsa",
Reactomeorganism = "human", OrgDb = "org.Hs.eg.db",
padjustvaluecutoff = 0.05, padjustedmethod = "BH")

Arguments

Modulelist	A list of miRNA sponge modules.
ont	One of "MF", "BP", and "CC" subontologies.
KEGGorganism	Organism, supported organism listed in http://www.genome.jp/kegg/catalog/org_list.html
Reactomeorganism	Organism, one of "human", "rat", "mouse", "celegans", "yeast", "zebrafish", "fly".
OrgDb	OrgDb
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 functional GO, KEGG and Reactome enrichment analysis results.

Author(s)

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

References

1. Yu G, Wang L, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology, 2012, 16(5):284-287.

2. Yu G and He Q. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems, 2016, 12(12), pp. 477-479.

Examples

## Not run: 
# Obtain expression data file "ExpData.csv" in csv format
ExpDatacsv <- system.file("extdata","ExpData.csv",package="miRspongeR")
ExpData <- read.csv(ExpDatacsv, header=TRUE, sep=",")

# 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=",")
pcceRInt <- spongeMethod(miRTarget, ExpData, method = "pc")
spongenetwork_Cluster <- netModule(pcceRInt[, 1:2])
sponge_Module_FEA <- moduleFEA(spongenetwork_Cluster)

## End(Not run)

zhangjunpeng411/miRsponge documentation built on Aug. 25, 2024, 4:32 p.m.