module_WGCNA: module_WGCNA

Description Usage Arguments Value Author(s) References Examples

View source: R/miRSM.R

Description

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

Usage

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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

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

zhangjunpeng411/miRSM documentation built on Nov. 28, 2020, 7 a.m.