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

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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.

Author
Renaud Gaujoux, Cathal Seoighe
Date of publication
2015-05-26 08:12:33
Maintainer
Renaud Gaujoux <renaud@tx.technion.ac.il>
License
GPL (>= 2)
Version
0.20.6
URLs

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