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.

AuthorSepp Hochreiter <hochreit@bioinf.jku.at>
Date of publicationNone
MaintainerSepp Hochreiter <hochreit@bioinf.jku.at>
LicenseLGPL (>= 2.1)
Version2.20.0
http://www.bioinf.jku.at/software/fabia/fabia.html

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

Functions

avini Man page
avini<- Man page
avini,Factorization-method Man page
avini<-,Factorization,numeric-method Man page
avini<-,Factorization,vector-method Man page
center Man page
center<- Man page
center,Factorization-method Man page
center<-,Factorization,numeric-method Man page
center<-,Factorization,vector-method Man page
estimateMode Man page
extractBic Man page
extractPlot Man page
fabi Man page
fabia Man page
fabiaDemo Man page
fabiap Man page
fabias Man page
fabiasp Man page
fabiaVersion Man page
Factorization Man page
Factorization,ANY-method Man page
Factorization-class Man page
Factorization,list-method,numeric-method,vector-method,matrix-me Man page
Factorization-method Man page
ini Man page
ini<- Man page
ini<-,Factorization,matrix-method Man page
ini,Factorization-method Man page
l Man page
l<- Man page
L Man page
L<- Man page
lapla Man page
lapla<- Man page
lapla<-,Factorization,matrix-method Man page
lapla,Factorization-method Man page
L<-,Factorization,matrix-method Man page
l,Factorization-method Man page
L,Factorization-method Man page
l<-,Factorization,numeric-method Man page
LZ Man page
LZ<- Man page
LZ<-,Factorization,matrix-method Man page
LZ,Factorization-method Man page
M Man page
M<- Man page
makeFabiaData Man page
makeFabiaDataBlocks Man page
makeFabiaDataBlocksPos Man page
makeFabiaDataPos Man page
matrixImagePlot Man page
M<-,Factorization,matrix-method Man page
M,Factorization-method Man page
mfsc Man page
n Man page
n<- Man page
n,Factorization-method Man page
n<-,Factorization,numeric-method Man page
nmfdiv Man page
nmfeu Man page
nmfsc Man page
p1 Man page
p1<- Man page
p1,Factorization-method Man page
p1<-,Factorization,numeric-method Man page
p2 Man page
p2<- Man page
p2,Factorization-method Man page
p2<-,Factorization,numeric-method Man page
parameters Man page
parameters<- Man page
parameters<-,Factorization,list-method Man page
parameters,Factorization-method Man page
plotBicluster Man page
plot,Factorization-method Man page
plot,Factorization,missing-method Man page
projFunc Man page
projFuncPos Man page
Psi Man page
Psi<- Man page
Psi,Factorization-method Man page
Psi<-,Factorization,numeric-method Man page
Psi<-,Factorization,vector-method Man page
readSamplesSpfabia Man page
readSpfabiaResult Man page
samplesPerFeature Man page
scaleData Man page
scaleData<- Man page
scaleData,Factorization-method Man page
scaleData<-,Factorization,numeric-method Man page
scaleData<-,Factorization,vector-method Man page
show,Factorization-method Man page
show,Factorization-method Man page
showSelected Man page
showSelected,Factorization-method Man page
showSelected,Factorization,numeric-method Man page
spfabia Man page
summary,Factorization-method Man page
U Man page
U<- Man page
U<-,Factorization,matrix-method Man page
U,Factorization-method Man page
X Man page
X<- Man page
xavini Man page
xavini<- Man page
xavini,Factorization-method Man page
xavini<-,Factorization,numeric-method Man page
xavini<-,Factorization,vector-method Man page
X<-,Factorization,matrix-method Man page
X,Factorization-method Man page
Z Man page
Z<- Man page
Z<-,Factorization,matrix-method Man page
Z,Factorization-method Man page

Files

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

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