module_CEA: module_CEA

In zhangjunpeng411/miRSM: Inferring miRNA sponge modules in heterogeneous data

module_CEA

Description

Cancer enrichment analysis of miRNA sponge modules using hypergeometric distribution test

Usage

module_CEA(ceRExp, mRExp = NULL, Cancergenes, Modulelist)

Arguments

ceRExp	A SummarizedExperiment object. ceRNA expression data: rows are samples and columns are ceRNAs.
mRExp	NULL (default) or 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-Zhang-2)

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 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 Sept. 23, 2024, 4:37 a.m.