module_CEA: module_CEA

Description Usage Arguments Value Author(s) References Examples

View source: R/miRSM.R

Description

Cancer enrichment analysis of miRNA sponge modules using hypergeometric distribution test

Usage

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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

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data(BRCASampleData)
modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp)
# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC)
miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget,
                        modulegenes_WGCNA, method = "SRVC",
                        SMC.cutoff = 0.01, RV_method = "RV")
miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]]
miRSM.CEA.pvalue <- module_CEA(ceRExp, mRExp, BRCA_genes, 
                              miRSM_WGCNA_SRVC_genes)

zhangjunpeng411/miRSM documentation built on Nov. 28, 2020, 7 a.m.