module_WGCNA {miRSM} | R Documentation |
Identification of co-expressed gene modules from matched ceRNA and mRNA expression data using WGCNA package
module_WGCNA( ceRExp, mRExp, RsquaredCut = 0.9, num.ModuleceRs = 2, num.ModulemRs = 2 )
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. |
GeneSetCollection object: a list of module genes.
Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008, 9:559.#'
data(BRCASampleData) modulegenes_WGCNA <- module_WGCNA(ceRExp[, seq_len(80)], mRExp[, seq_len(80)])