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Background

Nonnegative Matrix Factorization (NMF) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applications of NMF in bioinformatics have demonstrated its ability to extract meaningful information from high-dimensional data such as gene expression microarrays. Developments in NMF theory and applications have resulted in a variety of algorithms and methods. However, most NMF implementations have been on commercial platforms, while those that are freely available typically require programming skills. This limits their use by the wider research community.

Results

Our objective is to provide the bioinformatics community with an open-source, easy-to-use and unified interface to standard NMF algorithms, as well as with a simple framework to help implement and test new NMF methods. For that purpose, we have developed a package for the R/BioConductor platform. The package ports public code to R, and is structured to enable users to easily modify and/or add algorithms. It includes a number of published NMF algorithms and initialization methods and facilitates the combination of these to produce new NMF strategies. Commonly used benchmark data and visualization methods are provided to help in the comparison and interpretation of the results.

Conclusions

The NMF package helps realize the potential of Nonnegative Matrix Factorization, especially in bioinformatics, providing easy access to methods that have already yielded new insights in many applications.


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Version

Install

install.packages('NMF')

Monthly Downloads

8,771

Version

0.27

License

GPL (>= 2)

Maintainer

Nicolas Sauwen

Last Published

February 8th, 2024

Functions in NMF (0.27)

nmf_update.lee_R

NMF Algorithm/Updates for Frobenius Norm
NMF-deprecated

Deprecated Functions in the Package NMF
NMF-defunct

Defunct Functions and Classes in the NMF Package
NMFList-class

Class for Storing Heterogeneous NMF fits
NMFSeed-class

Base class that defines the interface for NMF seeding methods.
nmf_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence
NMF-class

Generic Interface for Nonnegative Matrix Factorisation Models
NMF-package

Algorithms and framework for Nonnegative Matrix Factorization (NMF).
NMFOffset-class

NMF Model - Nonnegative Matrix Factorization with Offset
NMFStrategy-class

Virtual Interface for NMF Algorithms
NMFstd-class

NMF Model - Standard model
NMFStrategyFunction-class

Interface for Single Function NMF Strategies
NMFns-class

NMF Model - Nonsmooth Nonnegative Matrix Factorization
NMFStrategy

Factory Method for NMFStrategy Objects
NMFfit-class

Base Class for to store Nonnegative Matrix Factorisation results
NMFfitX1-class

Structure for Storing the Best Fit Amongst Multiple NMF Runs
NMFfitX-class

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
NMFfitXn-class

Structure for Storing All Fits from Multiple NMF Runs
NMFStrategyIterative-class

Interface for Algorithms: Implementation for Iterative NMF Algorithms
NMFfitX

Factory Method for Multiple NMF Run Objects
advanced-NMF

Advanced Usage of the Package NMF
aheatmap

Annotated Heatmaps
nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS
.atrack

Annotation Tracks
aggregate.measure

Utility function to aggregate numerical quality measures from NMFfitXn objects.
getRNG1

Extracting RNG Data from NMF Objects
Strategy-class

Generic Strategy Class
algorithm,NMFList-method

Returns the method names used to compute the NMF fits in the list. It returns NULL if the list is empty.
summary

Assessing and Comparing NMF Models
algorithmic-NMF

Generic Interface for Algorithms
bioc-NMF

Specific NMF Layer for Bioconductor
ccBreaks

Generate Break Intervals from Numeric Variables
basiscor

Correlations in NMF Models
ccRamp

Builds a Color Ramp from Compact Color Specification
ccSpec

Extract Colour Palette Specification
basis

Accessing NMF Factors
checkErrors

Error Checks in NMF Runs
ccPalette

Builds a Color Palette from Compact Color Specification
canFit

Testing Compatibility of Algorithm and Models
c,NMF-method

Concatenating NMF Models
cutdendro

Fade Out the Upper Branches from a Dendrogram
basisnames

Dimension names for NMF objects
cluster_mat

Cluster Matrix Rows in Annotated Heatmaps
cophcor

Cophenetic Correlation Coefficient
deviance

Distances and Objective Functions
nbasis

Dimension of NMF Objects
connectivity

Clustering Connectivity and Consensus Matrices
consensushc

Hierarchical Clustering of a Consensus Matrix
consensus,NMFfitXn-method

Computes the consensus matrix of the set of fits stored in object, as the mean connectivity matrix across runs.
consensus,NMFfitX1-method

Returns the consensus matrix computed while performing all NMF runs, amongst which object was selected as the best fit.
tryViewport

Internal Grid Extension
.fcnnls

Internal Routine for Fast Combinatorial Nonnegative Least-Squares
esGolub

Golub ExpressionSet
gfile

Open a File Graphic Device
heatmap-NMF

Heatmaps of NMF Factors
fitted

Fitted Matrix in NMF Models
dispersion

Dispersion of a Matrix
fit

Extracting Fitted Models
registerDoBackend

Utilities and Extensions for Foreach Loops
fcnnls

Fast Combinatorial Nonnegative Least-Square
lverbose

Internal verbosity option
latex_preamble

LaTeX Utilities for Vignettes
nmfAlgorithm

Listing and Retrieving NMF Algorithms
match_atrack

Extending Annotation Vectors
isCRANcheck

Package Check Utils
nmf_update.lsnmf

Multiplicative Updates for LS-NMF
nmf

Running NMF algorithms
nmf.equal

Testing Equality of NMF Models
compare-NMF

Comparing Results from Different NMF Runs
pmax.inplace

Updating Objects In Place
nmfSeed

Seeding Strategies for NMF Algorithms
nmfApply

Apply Function for NMF Objects
nmfObject

Updating NMF Objects
nmfWrapper

Wrapping NMF Algorithms
nmfReport

Run NMF Methods and Generate a Report
nmfModel

Factory Methods NMF Models
nmfFormals

Showing Arguments of NMF Algorithms
nmfEstimateRank

Estimate Rank for NMF Models
nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence
nmfCheck

Checking NMF Algorithm
objective,NMFfit-method

Returns the objective function associated with the algorithm that computed the fitted NMF model object, or the objective value with respect to a given target matrix y if it is supplied.
parallel-NMF

Utilities for Parallel Computations
nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance
offset,NMFOffset-method

Offsets in NMF Models with Offset
nneg

Transforming from Mixed-sign to Nonnegative Data
nmf_update.ns

NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
options-NMF

NMF Package Specific Options
nmf_update.euclidean_offset.h

NMF Multiplicative Update for NMF with Offset Models
offset,NMFfit-method

Returns the offset from the fitted model.
parse_formula

Simple Parsing of Formula
rmatrix

Generating Random Matrices
predict

Clustering and Prediction
rnmf

Generating Random NMF Models
randomize

Randomizing Data
purity

Purity and Entropy of a Clustering
plot,NMFfit,missing-method

Plots the residual track computed at regular interval during the fit of the NMF model x.
residuals

Residuals in NMF Models
profplot

Plotting Expression Profiles
methods-NMF

Registry for NMF Algorithms
revPalette

Flags a Color Palette Specification for Reversion
runtime.all,NMFfitXn-method

Returns the CPU time used to perform all the NMF fits stored in object.
NMFSeed

NMFSeed is a constructor method that instantiate NMFSeed objects.
setNMFMethod

Registering NMF Algorithms
scale.NMF

Rescaling NMF Models
silhouette.NMF

Silhouette of NMF Clustering
show,NMFfitXn-method

Show method for objects of class NMFfitXn
show,NMFfitX-method

Show method for objects of class NMFfitX
show,NMFns-method

Show method for objects of class NMFns
show,NMFfit-method

Show method for objects of class NMFfit
show,NMFfitX1-method

Show method for objects of class NMFfitX1
show,NMFStrategyIterative-method

Show method for objects of class NMFStrategyIterative
rss

Residual Sum of Squares and Explained Variance
seed

Interface for NMF Seeding Methods
syntheticNMF

Simulating Datasets
staticVar

Get/Set a Static Variable in NMF Algorithms
t.NMF

Transformation NMF Model Objects
runtime,NMFList-method

Returns the CPU time required to compute all NMF fits in the list. It returns NULL if the list is empty. If no timing data are available, the sequential time is returned.
show,NMFOffset-method

Show method for objects of class NMFOffset
show,NMFSeed-method

Show method for objects of class NMFSeed
show,NMF-method

Show method for objects of class NMF
show,NMFList-method

Show method for objects of class NMFList
featureScore

Feature Selection in NMF Models
smoothing

Smoothing Matrix in Nonsmooth NMF Models
NMFStop

Stopping Criteria for NMF Iterative Strategies
is.nmf

Testing NMF Objects
utils-NMF

Utility Function in the NMF Package
[,NMF-method

Sub-setting NMF Objects
sparseness

Sparseness
txtProgressBar

Simple Progress Bar
setupBackend

Computational Setup Functions
ibterms

Fixed Terms in NMF Models
bterms<-

Fixed Terms in NMF Models