module_miRsponge {miRSM}

R Documentation

module_miRsponge

Description

Extract miRNA sponge interactions of each miRNA sponge module

Usage

module_miRsponge(ceRExp, mRExp, 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.
Modulelist	List object: a list of the identified miRNA sponge modules.

Value

List object: miRNA sponge interactions of each miRNA sponge module.

Author(s)

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

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_WGCNA_share_miRs <-  share_miRs(miRExp, ceRExp, mRExp, 
                                      miRTarget, miRSM_WGCNA_SRVC_genes)
miRSM_WGCNA_miRsponge <- module_miRsponge(ceRExp, mRExp, 
                                         miRSM_WGCNA_SRVC_genes)

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