# NMF v0.21.0

Monthly downloads

## 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.

## 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 |

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