module_biclust {miRSM} | R Documentation |
Identification of gene modules from matched ceRNA and mRNA expression data using a series of biclustering packages, including biclust, runibic, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR and rqubic
module_biclust(ceRExp, mRExp, BCmethod = "fabia", 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. |
BCmethod |
Specification of the biclustering method, including 'BCBimax', 'BCCC', 'BCPlaid' (default), 'BCQuest', 'BCSpectral', 'BCXmotifs', 'BCUnibic', iBBiG', 'fabia', 'fabiap', 'fabias', 'mfsc', 'nmfdiv', 'nmfeu', 'nmfsc', 'FLOC', 'isa', 'BCs4vd', 'BCssvd', 'bibit' and 'quBicluster'. |
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)
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data(BRCASampleData) modulegenes_biclust <- module_biclust(ceRExp[, seq_len(30)], mRExp[, seq_len(30)])