module_biclust: module_biclust

In miRSM: Inferring miRNA sponge modules in heterogeneous data

Description

Identification of gene modules from matched ceRNA and mRNA expression data using a series of biclustering packages, including biclust, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR and rqubic

Usage

module_biclust(
  ceRExp,
  mRExp,
  BCmethod = "fabia",
  num.modules = 10,
  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.
BCmethod	Specification of the biclustering method, including 'BCBimax', 'BCCC', 'BCPlaid' (default), 'BCQuest', 'BCSpectral', 'BCXmotifs', iBBiG', 'fabia', 'fabiap', 'fabias', 'mfsc', 'nmfdiv', 'nmfeu', 'nmfsc', 'FLOC', 'isa', 'BCs4vd', 'BCssvd', 'bibit' and 'quBicluster'.
num.modules	The number of modules to be identified. For the 'BCPlaid', 'BCSpectral', 'isa' and 'bibit' methods, no need to set the parameter. For the 'quBicluster' method, the parameter is used to set the number of biclusters that should be reported.
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

Preli\'c A, Bleuler S, Zimmermann P, Wille A, B\'uhlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E. A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics. 2006, 22(9):1122-9.

Cheng Y, Church GM. Biclustering of expression data. Proc Int Conf Intell Syst Mol Biol. 2000, 8:93-103.

Turner H, Bailey T, Krzanowski W. Improved biclustering of microarray data demonstrated through systematic performance tests. Comput Stat Data Anal. 2003, 48(2): 235-254.

Murali TM, Kasif S. Extracting conserved gene expression motifs from gene expression data. Pac Symp Biocomput. 2003:77-88.

Kluger Y, Basri R, Chang JT, Gerstein M. Spectral biclustering of microarray data: coclustering genes and conditions. Genome Res. 2003, 13(4):703-16.

Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane AC. iBBiG: iterative binary bi-clustering of gene sets. Bioinformatics. 2012, 28(19):2484-92.

Hochreiter S, Bodenhofer U, Heusel M, Mayr A, Mitterecker A, Kasim A, Khamiakova T, Van Sanden S, Lin D, Talloen W, Bijnens L, G\'ohlmann HW, Shkedy Z, Clevert DA. FABIA: factor analysis for bicluster acquisition. Bioinformatics. 2010, 26(12):1520-7.

Yang J, Wang H, Wang W, Yu, PS. An improved biclustering method for analyzing gene expression. Int J Artif Intell Tools. 2005, 14(5): 771-789.

Bergmann S, Ihmels J, Barkai N. Iterative signature algorithm for the analysis of large-scale gene expression data. Phys Rev E Stat Nonlin Soft Matter Phys. 2003, 67(3 Pt 1):031902.

Sill M, Kaiser S, Benner A, Kopp-Schneider A. Robust biclustering by sparse singular value decomposition incorporating stability selection. Bioinformatics. 2011, 27(15):2089-97.

Lee M, Shen H, Huang JZ, Marron JS. Biclustering via sparse singular value decomposition. Biometrics. 2010, 66(4):1087-95.

Rodriguez-Baena DS, Perez-Pulido AJ, Aguilar-Ruiz JS. A biclustering algorithm for extracting bit-patterns from binary datasets. Bioinformatics. 2011, 27(19):2738-45.

Li G, Ma Q, Tang H, Paterson AH, Xu Y. QUBIC: a qualitative biclustering algorithm for analyses of gene expression data. Nucleic Acids Res. 2009, 37(15):e101.

Examples

data(BRCASampleData)
modulegenes_biclust <- module_biclust(ceRExp[, seq_len(30)],
    mRExp[, seq_len(30)])

miRSM documentation built on April 16, 2021, 6 p.m.