module_NMF {miRSM} | R Documentation |
Identification of gene modules from matched ceRNA and mRNA expression data using NMF package
module_NMF( ceRExp, mRExp, NMF.algorithm = "brunet", num.modules = 10, 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. |
NMF.algorithm |
Specification of the NMF algorithm, including 'brunet' (default), 'Frobenius', 'KL', 'lee', 'nsNMF', 'offset', 'siNMF', 'snmf/l', 'snmf/r'. |
num.modules |
The number of modules to be identified. |
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)
Gaujoux R, Seoighe C. A flexible R package for nonnegative matrix factorization. BMC Bioinformatics. 2010, 11:367.
data(BRCASampleData) # Reimport NMF package to avoid conflicts with DelayedArray package library(NMF) modulegenes_NMF <- module_NMF(ceRExp[, seq_len(10)], mRExp[, seq_len(10)])