fabia: FABIA: Factor Analysis for Bicluster Acquisition

Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C.

Author
Sepp Hochreiter <hochreit@bioinf.jku.at>
Date of publication
None
Maintainer
Sepp Hochreiter <hochreit@bioinf.jku.at>
License
LGPL (>= 2.1)
Version
2.20.0
URLs

View on Bioconductor

Man pages

estimateMode
Estimation of the modes of the rows of a matrix
extractBic
Extraction of Biclusters
extractPlot
Plotting of Biclustering Results
fabi
Factor Analysis for Bicluster Acquisition: Laplace Prior...
fabia
Factor Analysis for Bicluster Acquisition: Laplace Prior...
fabiaDemo
Demos for fabia
fabiap
Factor Analysis for Bicluster Acquisition: Post-Projection...
fabias
Factor Analysis for Bicluster Acquisition: Sparseness...
fabiasp
Factor Analysis for Bicluster Acquisition: Sparseness...
fabiaVersion
Display version info for package and for FABIA
Factorization-class
Factorization instances
makeFabiaData
Generation of Bicluster Data
makeFabiaDataBlocks
Generation of Bicluster Data with Bicluster Blocks
makeFabiaDataBlocksPos
Generation of Bicluster Data with Bicluster Blocks
makeFabiaDataPos
Generation of Bicluster Data
matrixImagePlot
Plotting of a Matrix
mfsc
Sparse Matrix Factorization for Bicluster Analysis (MFSC)
nmfdiv
Non-negative Matrix Factorization: Kullback-Leibler...
nmfeu
Non-negative Matrix Factorization: Euclidean Distance
nmfsc
Non-negative Sparse Matrix Factorization
plotBicluster
Plotting of a bicluster
projFunc
Projection of a Vector to a Sparse Vector
projFuncPos
Projection of a Vector to a Non-negative Sparse Vector
readSamplesSpfabia
Factor Analysis for Bicluster Acquisition: Read Sparse Matrix...
readSpfabiaResult
Factor Analysis for Bicluster Acquisition: Read Results of...
samplesPerFeature
Factor Analysis for Bicluster Acquisition: Supplies samples...
spfabia
Factor Analysis for Bicluster Acquisition: SPARSE FABIA

Files in this package

fabia/DESCRIPTION
fabia/NAMESPACE
fabia/NEWS
fabia/R
fabia/R/AllClasses.R
fabia/R/AllGenerics.R
fabia/R/fabia.R
fabia/R/methods-Factorization-class.R
fabia/R/zzz.R
fabia/build
fabia/build/vignette.rds
fabia/cleanup
fabia/configure
fabia/configure.ac
fabia/configure.win
fabia/demo
fabia/demo/00Index
fabia/demo/demo01FabiaToydata.R
fabia/demo/demo02FabiaBreastcancer.R
fabia/demo/demo03FabiaMultipleTissues.R
fabia/demo/demo04FabiaLymphoma.R
fabia/demo/demo05FabiasToydata.R
fabia/demo/demo06FabiasBreastcancer.R
fabia/demo/demo07FabiasMultipleTissues.R
fabia/demo/demo08FabiasLymphoma.R
fabia/inst
fabia/inst/CITATION
fabia/inst/doc
fabia/inst/doc/fabia.R
fabia/inst/doc/fabia.Rnw
fabia/inst/doc/fabia.pdf
fabia/man
fabia/man/Factorization-class.Rd
fabia/man/estimateMode.Rd
fabia/man/extractBic.Rd
fabia/man/extractPlot.Rd
fabia/man/fabi.Rd
fabia/man/fabia.Rd
fabia/man/fabiaDemo.Rd
fabia/man/fabiaVersion.Rd
fabia/man/fabiap.Rd
fabia/man/fabias.Rd
fabia/man/fabiasp.Rd
fabia/man/makeFabiaData.Rd
fabia/man/makeFabiaDataBlocks.Rd
fabia/man/makeFabiaDataBlocksPos.Rd
fabia/man/makeFabiaDataPos.Rd
fabia/man/matrixImagePlot.Rd
fabia/man/mfsc.Rd
fabia/man/nmfdiv.Rd
fabia/man/nmfeu.Rd
fabia/man/nmfsc.Rd
fabia/man/plotBicluster.Rd
fabia/man/projFunc.Rd
fabia/man/projFuncPos.Rd
fabia/man/readSamplesSpfabia.Rd
fabia/man/readSpfabiaResult.Rd
fabia/man/samplesPerFeature.Rd
fabia/man/spfabia.Rd
fabia/src
fabia/src/Makefile.win
fabia/src/Makevars.in
fabia/src/fabiac.c
fabia/vignettes
fabia/vignettes/bioinf-article.txi
fabia/vignettes/bioinf-bar.png
fabia/vignettes/bioinf.cls
fabia/vignettes/fabia.Rnw
fabia/vignettes/fabia.bib
fabia/vignettes/fabia_defs.sty
fabia/vignettes/figures
fabia/vignettes/figures/fabia-lap1.eps
fabia/vignettes/figures/fabia-lap1.pdf
fabia/vignettes/figures/fabia-lap2.eps
fabia/vignettes/figures/fabia-lap2.pdf
fabia/vignettes/figures/vectors_1.eps
fabia/vignettes/figures/vectors_1.pdf
fabia/vignettes/natbib.bst
fabia/vignettes/natbib.sty