share_miRs {miRSM}R Documentation

share_miRs

Description

Extract common miRNAs of each miRNA sponge module

Usage

share_miRs(miRExp, ceRExp, mRExp, miRTarget, Modulelist)

Arguments

miRExp

A SummarizedExperiment object. miRNA expression data: rows are samples and columns are miRNAs.

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.

miRTarget

A SummarizedExperiment object. Putative miRNA-target binding information.

Modulelist

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

Value

List object: a list of common miRNAs 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 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_WGCNA_share_miRs <-  share_miRs(miRExp, ceRExp, mRExp, miRTarget, miRSM_WGCNA_CC_genes)


[Package miRSM version 1.2.1 Index]