fabia: FABIA: Factor Analysis for Bicluster Acquisition
Version 2.22.0

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>
Bioconductor views Clustering DifferentialExpression Microarray MultipleComparison StatisticalMethod Visualization
Date of publicationNone
MaintainerSepp Hochreiter <hochreit@bioinf.jku.at>
LicenseLGPL (>= 2.1)
Version2.22.0
URL http://www.bioinf.jku.at/software/fabia/fabia.html
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("fabia")

Popular man pages

extractPlot: Plotting of Biclustering Results
fabi: Factor Analysis for Bicluster Acquisition: Laplace Prior...
fabiaDemo: Demos for fabia
fabiap: Factor Analysis for Bicluster Acquisition: Post-Projection...
mfsc: Sparse Matrix Factorization for Bicluster Analysis (MFSC)
nmfeu: Non-negative Matrix Factorization: Euclidean Distance
plotBicluster: Plotting of a bicluster
See all...

All man pages Function index File listing

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

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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/fabia.R
R/methods-Factorization-class.R
R/zzz.R
build
build/vignette.rds
cleanup
configure
configure.ac
configure.win
demo
demo/00Index
demo/demo01FabiaToydata.R
demo/demo02FabiaBreastcancer.R
demo/demo03FabiaMultipleTissues.R
demo/demo04FabiaLymphoma.R
demo/demo05FabiasToydata.R
demo/demo06FabiasBreastcancer.R
demo/demo07FabiasMultipleTissues.R
demo/demo08FabiasLymphoma.R
inst
inst/CITATION
inst/doc
inst/doc/fabia.R
inst/doc/fabia.Rnw
inst/doc/fabia.pdf
man
man/Factorization-class.Rd
man/estimateMode.Rd
man/extractBic.Rd
man/extractPlot.Rd
man/fabi.Rd
man/fabia.Rd
man/fabiaDemo.Rd
man/fabiaVersion.Rd
man/fabiap.Rd
man/fabias.Rd
man/fabiasp.Rd
man/makeFabiaData.Rd
man/makeFabiaDataBlocks.Rd
man/makeFabiaDataBlocksPos.Rd
man/makeFabiaDataPos.Rd
man/matrixImagePlot.Rd
man/mfsc.Rd
man/nmfdiv.Rd
man/nmfeu.Rd
man/nmfsc.Rd
man/plotBicluster.Rd
man/projFunc.Rd
man/projFuncPos.Rd
man/readSamplesSpfabia.Rd
man/readSpfabiaResult.Rd
man/samplesPerFeature.Rd
man/spfabia.Rd
src
src/Makefile.win
src/Makevars.in
src/fabiac.c
vignettes
vignettes/bioinf-article.txi
vignettes/bioinf-bar.png
vignettes/bioinf.cls
vignettes/fabia.Rnw
vignettes/fabia.bib
vignettes/fabia_defs.sty
vignettes/figures
vignettes/figures/fabia-lap1.eps
vignettes/figures/fabia-lap1.pdf
vignettes/figures/fabia-lap2.eps
vignettes/figures/fabia-lap2.pdf
vignettes/figures/vectors_1.eps
vignettes/figures/vectors_1.pdf
vignettes/natbib.bst
vignettes/natbib.sty
fabia documentation built on May 20, 2017, 9:55 p.m.

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