module_CEA {miRSM}R Documentation

module_CEA

Description

Cancer enrichment analysis of miRNA sponge modules using hypergeometric distribution test

Usage

module_CEA(ceRExp, mRExp, Cancergenes, Modulelist)

Arguments

ceRExp

A SummarizedExperiment object. ceRNA expression data: rows are samples and columns are ceRNAs.

mRExp

A SummarizedExperiment object. mRNA expression data: rows are samples and columns are mRNAs.

Cancergenes

A SummarizedExperiment object: a list of cancer genes given.

Modulelist

List object: a list of the identified miRNA sponge modules.

Value

Cancer enrichment significance p-values of the identified miRNA sponge modules

Author(s)

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

References

Johnson NL, Kotz S, Kemp AW (1992) "Univariate Discrete Distributions", Second Edition. New York: Wiley.

Examples

data(BRCASampleData)
modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp)
# Identify miRNA sponge modules using canonical correlation (CC)
miRSM_WGCNA_CC <- miRSM(miRExp, ceRExp, mRExp, miRTarget,
                        modulegenes_WGCNA, nperms = 10, method = 'CC')
miRSM_WGCNA_CC_genes <- miRSM_WGCNA_CC[[2]]
miRSM.CEA.pvalue <- module_CEA(ceRExp, mRExp, BRCA_genes, miRSM_WGCNA_CC_genes)


[Package miRSM version 1.2.2 Index]