module_Coexpress {miRSM}R Documentation

module_Coexpress

Description

Co-expression analysis of each miRNA sponge module and its corresponding random miRNA sponge module

Usage

module_Coexpress(ceRExp, mRExp, Modulelist, resample = 1000,
  method = c("mean", "median"))

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.

resample

The number of random miRNA sponge modules generated, and 1000 times in default.

method

The method used to evaluate the co-expression level of each miRNA sponge module. Users can select "mean" or "median" to calculate co-expression value of each miRNA sponge module and its corresponding random miRNA sponge module.

Value

List object: co-expression values of miRNA sponge modules and their corresponding random miRNA sponge modules.

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_Coexpress <-  module_Coexpress(ceRExp, mRExp, miRSM_WGCNA_CC_genes, 
resample = 10, method = "mean")


[Package miRSM version 1.2.1 Index]