NMF v0.21.0

Monthly downloads

by Nicolas Sauwen View Source

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.

Readme

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.

Travis check:

Functions in NMF

Name	Description
nmf_update.lee_R	NMF Algorithm/Updates for Frobenius Norm
basiscor	Correlations in NMF Models
cophcor	Cophenetic Correlation Coefficient
bioc-NMF	Specific NMF Layer for Bioconductor
cutdendro	Fade Out the Upper Branches from a Dendrogram
heatmap-NMF	Heatmaps of NMF Factors
pmax.inplace	Updating Objects In Place
nmf	Running NMF algorithms
nmf.equal	Testing Equality of NMF Models
nmfFormals	Showing Arguments of NMF Algorithms
nmfModel	Factory Methods NMF Models
parse_formula	Simple Parsing of Formula
methods-NMF	Registry for NMF Algorithms
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
seed	Interface for NMF Seeding Methods
setNMFMethod	Registering NMF Algorithms
silhouette.NMF	Silhouette of NMF Clustering
smoothing	Smoothing Matrix in Nonsmooth NMF Models
ibterms	Fixed Terms in NMF Models
bterms<-	Fixed Terms in NMF Models
NMF-defunct	Defunct Functions and Classes in the NMF Package
NMF-class	Generic Interface for Nonnegative Matrix Factorisation Models
NMFns-class	NMF Model - Nonsmooth Nonnegative Matrix Factorization
NMFstd-class	NMF Model - Standard model
.atrack	Annotation Tracks
checkErrors	Error Checks in NMF Runs
basis	Accessing NMF Factors
deviance	Distances and Objective Functions
cluster_mat	Cluster Matrix Rows in Annotated Heatmaps
basisnames	Dimension names for NMF objects
NMFSeed-class	Base class that defines the interface for NMF seeding methods.
.fcnnls	Internal Routine for Fast Combinatorial Nonnegative Least-Squares
NMFStrategy-class	Virtual Interface for NMF Algorithms
esGolub	Golub ExpressionSet
match_atrack	Extending Annotation Vectors
NMFStrategyFunction-class	Interface for Single Function NMF Strategies
NMFStrategy	Factory Method for NMFStrategy Objects
compare-NMF	Comparing Results from Different NMF Runs
aheatmap	Annotated Heatmaps
nneg	Transforming from Mixed-sign to Nonnegative Data
nmf_update.ns	NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
algorithm,NMFList-method	Returns the method names used to compute the NMF fits in the list. It returns NULL if the list is empty.
NMF-deprecated	Deprecated Functions in the Package NMF
NMF-package	Algorithms and framework for Nonnegative Matrix Factorization (NMF).
NMFfitX-class	Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
options-NMF	NMF Package Specific Options
c,NMF-method	Concatenating NMF Models
canFit	Testing Compatibility of Algorithm and Models
consensus,NMFfitXn-method	Computes the consensus matrix of the set of fits stored in object, as the mean connectivity matrix across runs.
consensushc	Hierarchical Clustering of a Consensus Matrix
NMFfitX	Factory Method for Multiple NMF Run Objects
algorithmic-NMF	Generic Interface for Algorithms
gfile	Open a File Graphic Device
tryViewport	Internal Grid Extension
summary	Assessing and Comparing NMF Models
parallel-NMF	Utilities for Parallel Computations
ccBreaks	Generate Break Intervals from Numeric Variables
nmf_update.lsnmf	Multiplicative Updates for LS-NMF
ccPalette	Builds a Color Palette from Compact Color Specification
nbasis	Dimension of NMF Objects
lverbose	Internal verbosity option
NMFList-class	Class for Storing Heterogeneous NMF fits
randomize	Randomizing Data
purity	Purity and Entropy of a Clustering
NMFOffset-class	NMF Model - Nonnegative Matrix Factorization with Offset
NMFStrategyIterative-class	Interface for Algorithms: Implementation for Iterative NMF Algorithms
scale.NMF	Rescaling NMF Models
nmfSeed	Seeding Strategies for NMF Algorithms
NMFfit-class	Base Class for to store Nonnegative Matrix Factorisation results
nmfWrapper	Wrapping NMF Algorithms
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.
offset,NMFOffset-method	Offsets in NMF Models with Offset
getRNG1	Extracting RNG Data from NMF Objects
revPalette	Flags a Color Palette Specification for Reversion
nmfAlgorithm.SNMF_R	NMF Algorithm - Sparse NMF via Alternating NNLS
dispersion	Dispersion of a Matrix
rmatrix	Generating Random Matrices
ccRamp	Builds a Color Ramp from Compact Color Specification
fitted	Fitted Matrix in NMF Models
registerDoBackend	Utilities and Extensions for Foreach Loops
nmfAlgorithm	Listing and Retrieving NMF Algorithms
show,NMFOffset-method	Show method for objects of class NMFOffset
featureScore	Feature Selection in NMF Models
show,NMFSeed-method	Show method for objects of class NMFSeed
nmfApply	Apply Function for NMF Objects
ccSpec	Extract Colour Palette Specification
show,NMFfitX-method	Show method for objects of class NMFfitX
consensus,NMFfitX1-method	Returns the consensus matrix computed while performing all NMF runs, amongst which object was selected as the best fit.
is.nmf	Testing NMF Objects
connectivity	Clustering Connectivity and Consensus Matrices
show,NMFfitX1-method	Show method for objects of class NMFfitX1
txtProgressBar	Simple Progress Bar
show,NMFfitXn-method	Show method for objects of class NMFfitXn
show,NMFns-method	Show method for objects of class NMFns
fcnnls	Fast Combinatorial Nonnegative Least-Square
syntheticNMF	Simulating Datasets
t.NMF	Transformation NMF Model Objects
fit	Extracting Fitted Models
nmfCheck	Checking NMF Algorithm
nmfEstimateRank	Estimate Rank for NMF Models
nmf_update.KL.h	NMF Multiplicative Updates for Kullback-Leibler Divergence
nmfObject	Updating NMF Objects
nmf_update.euclidean.h	NMF Multiplicative Updates for Euclidean Distance
nmfReport	Run NMF Methods and Generate a Report
offset,NMFfit-method	Returns the offset from the fitted model.
nmf_update.euclidean_offset.h	NMF Multiplicative Update for NMF with Offset Models
profplot	Plotting Expression Profiles
predict	Clustering and Prediction
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.
rnmf	Generating Random NMF Models
runtime.all,NMFfitXn-method	Returns the CPU time used to perform all the NMF fits stored in object.
rss	Residual Sum of Squares and Explained Variance
show,NMFList-method	Show method for objects of class NMFList
show,NMF-method	Show method for objects of class NMF
show,NMFStrategyIterative-method	Show method for objects of class NMFStrategyIterative
show,NMFfit-method	Show method for objects of class NMFfit
utils-NMF	Utility Function in the NMF Package
NMFSeed	NMFSeed is a constructor method that instantiate NMFSeed objects.
setupBackend	Computational Setup Functions
staticVar	Get/Set a Static Variable in NMF Algorithms
sparseness	Sparseness
NMFStop	Stopping Criteria for NMF Iterative Strategies
[,NMF-method	Sub-setting NMF Objects
nmf_update.brunet_R	NMF Algorithm/Updates for Kullback-Leibler Divergence
NMFfitXn-class	Structure for Storing All Fits from Multiple NMF Runs
NMFfitX1-class	Structure for Storing the Best Fit Amongst Multiple NMF Runs
Strategy-class	Generic Strategy Class
advanced-NMF	Advanced Usage of the Package NMF
No Results!

Vignettes of NMF

Name
src/bmc.R
NMF-vignette.Rnw
consensus.pdf
heatmaps.Rnw
No Results!

Last month downloads

Details

Type	Package
Date	2018-02-18
License	GPL (>= 2)
URL	http://renozao.github.io/NMF
LazyLoad	yes
VignetteBuilder	knitr
Collate	'colorcode.R' 'options.R' 'grid.R' 'atracks.R' 'aheatmap.R' 'algorithmic.R' 'nmf-package.R' 'rmatrix.R' 'utils.R' 'versions.R' 'NMF-class.R' 'transforms.R' 'Bioc-layer.R' 'NMFstd-class.R' 'NMFOffset-class.R' 'heatmaps.R' 'NMFns-class.R' 'nmfModel.R' 'fixed-terms.R' 'NMFfit-class.R' 'NMFSet-class.R' 'NMFStrategy-class.R' 'registry.R' 'NMFSeed-class.R' 'NMFStrategyFunction-class.R' 'NMFStrategyIterative-class.R' 'NMFplots.R' 'registry-algorithms.R' 'algorithms-base.R' 'algorithms-lnmf.R' 'algorithms-lsnmf.R' 'algorithms-pe-nmf.R' 'algorithms-siNMF.R' 'algorithms-snmf.R' 'data.R' 'extractFeatures.R' 'parallel.R' 'registry-seed.R' 'nmf.R' 'rnmf.R' 'run.R' 'seed-base.R' 'seed-ica.R' 'seed-nndsvd.R' 'setNMFClass.R' 'simulation.R' 'tests.R'
Packaged	2018-03-06 09:53:11 UTC; nsauwen
NeedsCompilation	yes
Repository	CRAN
Date/Publication	2018-03-06 16:35:36 UTC
RoxygenNote	6.0.1

suggests	bibtex , bigmemory (>= 4.2) , Biobase , corpcor , devtools , doMPI , fastICA , knitr , mail , RUnit , synchronicity (>= 1.3.2) , xtable
depends	cluster , methods , pkgmaker (>= 0.20) , R (>= 3.0.0) , registry , rngtools (>= 1.2.3) , utils
imports	colorspace , digest , doParallel , foreach , ggplot2 , graphics , grDevices , grid , gridBase , RColorBrewer , reshape2 , stats , stringr (>= 1.0.0)
Contributors	Renaud Gaujoux, Cathal Seoighe