NMF: Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
Version 0.20.6

Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

AuthorRenaud Gaujoux, Cathal Seoighe
Date of publication2015-05-26 08:12:33
MaintainerRenaud Gaujoux <renaud@tx.technion.ac.il>
LicenseGPL (>= 2)
Version0.20.6
URL http://renozao.github.io/NMF
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("NMF")

Getting started

Package overview
README.md

Popular man pages

aheatmap: Annotated Heatmaps
canFit: Testing Compatibility of Algorithm and Models
connectivity: Clustering Connectivity and Consensus Matrices
consensushc: Hierarchical Clustering of a Consensus Matrix
cophcor: Cophenetic Correlation Coefficient
grid: Internal Grid Extension
nmfEstimateRank: Estimate Rank for NMF Models
See all...

All man pages Function index File listing

Man pages

advanced: Advanced Usage of the Package NMF
aheatmap: Annotated Heatmaps
algorithm-commaNMFList-method: Returns the method names used to compute the NMF fits in the...
algorithm-commaNMFStrategyOctave-method: Returns the name of the Octave/Matlab function that...
algorithmic: Generic Interface for Algorithms
assess: Assessing and Comparing NMF Models
atrack: Annotation Tracks
basis-coef-methods: Accessing NMF Factors
basiscor: Correlations in NMF Models
bioc: Specific NMF Layer for Bioconductor
canFit: Testing Compatibility of Algorithm and Models
ccBreaks: Generate Break Intervals from Numeric Variables
c-commaNMF-method: Concatenating NMF Models
ccPalette: Builds a Color Palette from Compact Color Specification
ccRamp: Builds a Color Ramp from Compact Color Specification
ccSpec: Extract Colour Palette Specification
checkErrors: Error Checks in NMF Runs
cluster_mat: Cluster Matrix Rows in Annotated Heatmaps
connectivity: Clustering Connectivity and Consensus Matrices
consensus-commaNMFfitX1-method: Returns the consensus matrix computed while performing all...
consensus-commaNMFfitXn-method: Computes the consensus matrix of the set of fits stored in...
consensushc: Hierarchical Clustering of a Consensus Matrix
cophcor: Cophenetic Correlation Coefficient
cutdendro: Fade Out the Upper Branches from a Dendrogram
deviance: Distances and Objective Functions
dimnames: Dimension names for NMF objects
dims: Dimension of NMF Objects
dispersion: Dispersion of a Matrix
dot-fcnnls: Internal Routine for Fast Combinatorial Nonnegative...
esGolub: Golub ExpressionSet
fcnnls: Fast Combinatorial Nonnegative Least-Square
fit: Extracting Fitted Models
fitted: Fitted Matrix in NMF Models
foreach: Utilities and Extensions for Foreach Loops
Frobenius-nmf: NMF Algorithm/Updates for Frobenius Norm
gfile: Open a File Graphic Device
grid: Internal Grid Extension
heatmaps: Heatmaps of NMF Factors
inplace: Updating Objects In Place
KL-nmf: NMF Algorithm/Updates for Kullback-Leibler Divergence
lsNMF-nmf: Multiplicative Updates for LS-NMF
lverbose: Internal verbosity option
match_atrack: Extending Annotation Vectors
nmf: Running NMF algorithms
nmfAlgorithm: Listing and Retrieving NMF Algorithms
nmfApply: Apply Function for NMF Objects
nmfCheck: Checking NMF Algorithm
NMF-class: Generic Interface for Nonnegative Matrix Factorisation Models
nmf-compare: Comparing Results from Different NMF Runs
NMF-defunct: Defunct Functions and Classes in the NMF Package
NMF-deprecated: Deprecated Functions in the Package NMF
nmf.equal: Testing Equality of NMF Models
nmfEstimateRank: Estimate Rank for NMF Models
NMFfit-class: Base Class for to store Nonnegative Matrix Factorisation...
NMFfitX: Factory Method for Multiple NMF Run Objects
NMFfitX1-class: Structure for Storing the Best Fit Amongst Multiple NMF Runs
NMFfitX-class: Virtual Class to Handle Results from Multiple Runs of NMF...
NMFfitXn-class: Structure for Storing All Fits from Multiple NMF Runs
nmfFormals: Showing Arguments of NMF Algorithms
NMFList-class: Class for Storing Heterogeneous NMF fits
nmfModel: Factory Methods NMF Models
NMFns-class: NMF Model - Nonsmooth Nonnegative Matrix Factorization
nmfObject: Updating NMF Objects
NMFOffset-class: NMF Model - Nonnegative Matrix Factorization with Offset
NMF-package: Algorithms and framework for Nonnegative Matrix Factorization...
nmfReport: Run NMF Methods and Generate a Report
nmfSeed: Seeding Strategies for NMF Algorithms
NMFSeed-class: Base class that defines the interface for NMF seeding...
NMFstd-class: NMF Model - Standard model
NMFStrategy: Factory Method for NMFStrategy Objects
NMFStrategy-class: Virtual Interface for NMF Algorithms
NMFStrategyFunction-class: Interface for Single Function NMF Strategies
NMFStrategyIterative-class: Interface for Algorithms: Implementation for Iterative NMF...
NMFStrategyOctave-class: S4 Interface for Octave-Matlab NMF Algorithms
nmf_update_euclidean: NMF Multiplicative Updates for Euclidean Distance
nmf_update_KL: NMF Multiplicative Updates for Kullback-Leibler Divergence
nmfWrapper: Wrapping NMF Algorithms
nneg: Transforming from Mixed-sign to Nonnegative Data
nsNMF-nmf: NMF Multiplicative Update for Nonsmooth Nonnegative Matrix...
objective-commaNMFfit-method: Returns the objective function associated with the algorithm...
offset-commaNMFfit-method: Returns the offset from the fitted model.
offset-commaNMFOffset-method: Offsets in NMF Models with Offset
offset-nmf: NMF Multiplicative Update for NMF with Offset Models
options: NMF Package Specific Options
parallel: Utilities for Parallel Computations
parse_formula: Simple Parsing of Formula
plot-commaNMFfit-commamissing-method: Plots the residual track computed at regular interval during...
predict: Clustering and Prediction
profplot: Plotting Expression Profiles
purity: Purity and Entropy of a Clustering
randomize: Randomizing Data
registry-algorithm: Registry for NMF Algorithms
residuals: Residuals in NMF Models
revPalette: Flags a Color Palette Specification for Reversion
rmatrix: Generating Random Matrices
RNG: Extracting RNG Data from NMF Objects
rnmf: Generating Random NMF Models
rss: Residual Sum of Squares and Explained Variance
runtime.all-commaNMFfitXn-method: Returns the CPU time used to perform all the NMF fits stored...
runtime-commaNMFList-method: Returns the CPU time required to compute all NMF fits in the...
scale.NMF: Rescaling NMF Models
scores: Feature Selection in NMF Models
seed: Interface for NMF Seeding Methods
setNMFMethod: Registering NMF Algorithms
setNMFSeed: 'NMFSeed' is a constructor method that instantiate 'NMFSeed'...
setup: Computational Setup Functions
show-commaNMFfit-method: Show method for objects of class 'NMFfit'
show-commaNMFfitX1-method: Show method for objects of class 'NMFfitX1'
show-commaNMFfitX-method: Show method for objects of class 'NMFfitX'
show-commaNMFfitXn-method: Show method for objects of class 'NMFfitXn'
show-commaNMFList-method: Show method for objects of class 'NMFList'
show-commaNMF-method: Show method for objects of class 'NMF'
show-commaNMFns-method: Show method for objects of class 'NMFns'
show-commaNMFOffset-method: Show method for objects of class 'NMFOffset'
show-commaNMFSeed-method: Show method for objects of class 'NMFSeed'
show-commaNMFStrategyIterative-method: Show method for objects of class 'NMFStrategyIterative'
silhouette.NMF: Silhouette of NMF Clustering
smoothing: Smoothing Matrix in Nonsmooth NMF Models
SNMF-nmf: NMF Algorithm - Sparse NMF via Alternating NNLS
sparseness: Sparseness
staticVar: Get/Set a Static Variable in NMF Algorithms
stop-NMF: Stopping Criteria for NMF Iterative Strategies
Strategy-class: Generic Strategy Class
subset-NMF: Sub-setting NMF Objects
syntheticNMF: Simulating Datasets
terms: Fixed Terms in NMF Models
terms-internal: Fixed Terms in NMF Models
t.NMF: Transformation NMF Model Objects
txtProgressBar: Simple Progress Bar
types: Testing NMF Objects
utils: Utility Function in the NMF Package

Functions

Files

TODO
inst
inst/CITATION
inst/REFERENCES.bib
inst/tests
inst/tests/runit.NMFfit-class.r
inst/tests/runit.interface.r
inst/tests/runit.aheatmap.R
inst/tests/runit.NMFSet.r
inst/tests/runit.bioc.r
inst/tests/runit.NMFclass.r
inst/tests/runit.distance.r
inst/tests/runit.utils.r
inst/tests/runit.NMFStrategy-class.r
inst/tests/runit.parallel.r
inst/tests/runit.options.r
inst/tests/runit.algorithms.r
inst/tests/runit.seed.r
inst/scripts
inst/scripts/report.Rmd
inst/scripts/grid.R
inst/doc
inst/doc/heatmaps.Rnw
inst/doc/NMF-unitTests.Rnw
inst/doc/NMF-vignette.R
inst/doc/NMF-unitTests.R
inst/doc/NMF-unitTests.pdf
inst/doc/consensus.pdf
inst/doc/NMF-vignette.pdf
inst/doc/heatmaps.pdf
inst/doc/NMF-vignette.Rnw
inst/doc/heatmaps.R
inst/m-files
inst/m-files/brunet.R
inst/m-files/brunet-run.m
inst/m-files/brunet.m
tests
tests/doRUnit.R
src
src/divergence.cpp
src/euclidean.cpp
src/utils.cpp
src/distance.cpp
NAMESPACE
demo
demo/aheatmap.R
demo/00Index
demo/nmf.R
demo/heatmaps.R
NEWS
data
data/esGolub.rda
R
R/extractFeatures.R
R/Bioc-layer.R
R/utils.R
R/NMFStrategy-class.R
R/atracks.R
R/registry.R
R/algorithms-brunet.R
R/parallel.R
R/seed-base.R
R/versions.R
R/NMFSet-class.R
R/NMFOffset-class.R
R/nmfModel.R
R/registry-seed.R
R/NMFstd-class.R
R/NMFns-class.R
R/aheatmap.R
R/NMFStrategyIterative-class.R
R/NMFplots.R
R/data.R
R/simulation.R
R/seed-ica.R
R/setNMFClass.R
R/algorithms-base.R
R/options.R
R/NMF-class.R
R/NMFStrategyFunction-class.R
R/colorcode.R
R/algorithms-lnmf.R
R/run.R
R/NMFSeed-class.R
R/algorithms-snmf.R
R/NMFStrategyOctave-class.R
R/nmf.R
R/registry-algorithms.R
R/seed-nndsvd.R
R/rmatrix.R
R/algorithmic.R
R/rnmf.R
R/nmf-package.R
R/grid.R
R/fixed-terms.R
R/transforms.R
R/NMFfit-class.R
R/algorithms-pe-nmf.R
R/algorithms-siNMF.R
R/algorithms-lsnmf.R
R/heatmaps.R
R/tests.R
vignettes
vignettes/heatmaps.Rnw
vignettes/NMF-unitTests.Rnw
vignettes/src
vignettes/src/bmc.R
vignettes/consensus.pdf
vignettes/.install_extras
vignettes/NMF-vignette.Rnw
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/smoothing.Rd
man/offset-nmf.Rd
man/txtProgressBar.Rd
man/setNMFSeed.Rd
man/silhouette.NMF.Rd
man/cophcor.Rd
man/consensus-commaNMFfitX1-method.Rd
man/NMFfitX-class.Rd
man/fit.Rd
man/bioc.Rd
man/NMF-package.Rd
man/staticVar.Rd
man/seed.Rd
man/show-commaNMFStrategyIterative-method.Rd
man/advanced.Rd
man/nmf.Rd
man/types.Rd
man/setNMFMethod.Rd
man/NMFList-class.Rd
man/nmf.equal.Rd
man/terms-internal.Rd
man/lsNMF-nmf.Rd
man/deviance.Rd
man/offset-commaNMFOffset-method.Rd
man/residuals.Rd
man/NMFfitXn-class.Rd
man/NMFstd-class.Rd
man/checkErrors.Rd
man/nmfWrapper.Rd
man/nmfModel.Rd
man/scores.Rd
man/nsNMF-nmf.Rd
man/show-commaNMFfitX-method.Rd
man/show-commaNMFfitXn-method.Rd
man/parse_formula.Rd
man/algorithm-commaNMFList-method.Rd
man/nmfApply.Rd
man/ccBreaks.Rd
man/show-commaNMFfit-method.Rd
man/nmfObject.Rd
man/profplot.Rd
man/NMFSeed-class.Rd
man/runtime.all-commaNMFfitXn-method.Rd
man/nmfEstimateRank.Rd
man/basiscor.Rd
man/subset-NMF.Rd
man/revPalette.Rd
man/rss.Rd
man/show-commaNMFOffset-method.Rd
man/connectivity.Rd
man/rmatrix.Rd
man/parallel.Rd
man/plot-commaNMFfit-commamissing-method.Rd
man/Strategy-class.Rd
man/ccPalette.Rd
man/offset-commaNMFfit-method.Rd
man/nmf_update_KL.Rd
man/nmfCheck.Rd
man/aheatmap.Rd
man/utils.Rd
man/rnmf.Rd
man/assess.Rd
man/cutdendro.Rd
man/predict.Rd
man/randomize.Rd
man/algorithm-commaNMFStrategyOctave-method.Rd
man/NMFStrategyIterative-class.Rd
man/NMF-defunct.Rd
man/nmf_update_euclidean.Rd
man/options.Rd
man/nneg.Rd
man/ccSpec.Rd
man/NMF-class.Rd
man/SNMF-nmf.Rd
man/cluster_mat.Rd
man/NMFStrategy-class.Rd
man/sparseness.Rd
man/KL-nmf.Rd
man/c-commaNMF-method.Rd
man/basis-coef-methods.Rd
man/NMFns-class.Rd
man/NMF-deprecated.Rd
man/consensus-commaNMFfitXn-method.Rd
man/nmfFormals.Rd
man/lverbose.Rd
man/fcnnls.Rd
man/NMFStrategyFunction-class.Rd
man/purity.Rd
man/nmf-compare.Rd
man/NMFOffset-class.Rd
man/heatmaps.Rd
man/NMFStrategyOctave-class.Rd
man/dims.Rd
man/nmfReport.Rd
man/stop-NMF.Rd
man/inplace.Rd
man/algorithmic.Rd
man/runtime-commaNMFList-method.Rd
man/show-commaNMFns-method.Rd
man/scale.NMF.Rd
man/atrack.Rd
man/grid.Rd
man/foreach.Rd
man/fitted.Rd
man/gfile.Rd
man/canFit.Rd
man/ccRamp.Rd
man/terms.Rd
man/dispersion.Rd
man/consensushc.Rd
man/match_atrack.Rd
man/show-commaNMFfitX1-method.Rd
man/dimnames.Rd
man/registry-algorithm.Rd
man/NMFfit-class.Rd
man/show-commaNMFSeed-method.Rd
man/setup.Rd
man/show-commaNMF-method.Rd
man/syntheticNMF.Rd
man/nmfSeed.Rd
man/objective-commaNMFfit-method.Rd
man/show-commaNMFList-method.Rd
man/NMFfitX.Rd
man/dot-fcnnls.Rd
man/NMFfitX1-class.Rd
man/RNG.Rd
man/NMFStrategy.Rd
man/Frobenius-nmf.Rd
man/esGolub.Rd
man/t.NMF.Rd
man/nmfAlgorithm.Rd
.Rinstignore
NMF documentation built on May 19, 2017, 7:20 a.m.

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