module_WGCNA: module_WGCNA

In zhangjunpeng411/miRSM: Inferring miRNA sponge modules in heterogeneous data

module_WGCNA

Description

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

Usage

module_WGCNA(
  ceRExp,
  mRExp = NULL,
  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	NULL (default) or 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-Zhang-2)

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)])

zhangjunpeng411/miRSM documentation built on Sept. 23, 2024, 4:37 a.m.