module_WGCNA {miRSM}R Documentation

module_WGCNA

Description

Identification of co-expressed gene modules from matched ceRNA and mRNA expression data using WGCNA package

Usage

module_WGCNA(ceRExp, mRExp, RsquaredCut = 0.9, num.ModuleceRs = 2,
  num.ModulemRs = 2)

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.

RsquaredCut

Desired minimum scale free topology fitting index R^2 with interval [0 1].

num.ModuleceRs

The minimum number of ceRNAs in each module.

num.ModulemRs

The minimum number of mRNAs in each module.

Value

GeneSetCollection object: a list of module genes.

Author(s)

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

References

Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008, 9:559.#'

Examples

data(BRCASampleData)
modulegenes_WGCNA <- module_WGCNA(ceRExp[, seq_len(80)], 
    mRExp[, seq_len(80)])


[Package miRSM version 1.0.0 Index]