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

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
http://renozao.github.io/NMF

View on CRAN

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

Files in this package

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

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