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NMF (version 0.20.5)

Algorithms and framework for Nonnegative Matrix Factorization (NMF)

Description

This package provides a framework to perform Non-negative Matrix Factorization (NMF). It 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.

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Version

Install

install.packages('NMF')

Monthly Downloads

13,048

Version

0.20.5

License

GPL (>= 2)

Maintainer

Renaud Gaujoux

Last Published

March 18th, 2014

Functions in NMF (0.20.5)

Annotation Tracks

Assessing and Comparing NMF Models

algorithmic-NMF

Generic Interface for Algorithms

Extracting RNG Data from NMF Objects

consensus,NMFfitXn-method

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

registerDoBackend

Utilities and Extensions for Foreach Loops

Fast Combinatorial Nonnegative Least-Square

Utilities for Parallel Computations

Cluster Matrix Rows in Annotated Heatmaps

Internal Grid Extension

Simple Parsing of Formula

nmf_update.euclidean_offset.h

NMF Multiplicative Update for NMF with Offset Models

Generating Random Matrices

show,NMFfitX-method

Show method for objects of class NMFfitX

show,NMFStrategyIterative-method

Show method for objects of class NMFStrategyIterative

Testing Compatibility of Algorithm and Models

Base class that defines the interface for NMF seeding methods.

nmf_update.lee_R

NMF Algorithm/Updates for Frobenius Norm

consensus,NMFfitX1-method

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

Internal Routine for Fast Combinatorial Nonnegative Least-Squares

Testing Equality of NMF Models

Updating Objects In Place

Listing and Retrieving NMF Algorithms

Wrapping NMF Algorithms

Dispersion of a Matrix

Interface for NMF Seeding Methods

Rescaling NMF Models

Transformation NMF Model Objects

Silhouette of NMF Clustering

show,NMFList-method

Show method for objects of class NMFList

Utility Function in the NMF Package

Fade Out the Upper Branches from a Dendrogram

Advanced Usage of the Package NMF

Extending Annotation Vectors

nmfEstimateRank

Estimate Rank for NMF Models

Transforming from Mixed-sign to Nonnegative Data

Registry for NMF Algorithms

Smoothing Matrix in Nonsmooth NMF Models

Simulating Datasets

Fixed Terms in NMF Models

Specific NMF Layer for Bioconductor

Generic Interface for Nonnegative Matrix Factorisation Models

Concatenating NMF Models

Extract Colour Palette Specification

Checking NMF Algorithm

Distances and Objective Functions

Stopping Criteria for NMF Iterative Strategies

Seeding Strategies for NMF Algorithms

nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance

NMFStrategyFunction-class

Interface for Single Function NMF Strategies

Factory Method for Multiple NMF Run Objects

Annotated Heatmaps

Correlations in NMF Models

Hierarchical Clustering of a Consensus Matrix

Extracting Fitted Models

Cophenetic Correlation Coefficient

offset,NMFfit-method

Returns the offset from the fitted model.

NMF Package Specific Options

Residuals in NMF Models

Feature Selection in NMF Models

Get/Set a Static Variable in NMF Algorithms

show,NMFfitXn-method

Show method for objects of class NMFfitXn

Fixed Terms in NMF Models

Deprecated Functions in the Package NMF

Factory Method for NMFStrategy Objects

Algorithms and framework for Nonnegative Matrix Factorization (NMF).

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms

NMFStrategyOctave-class

S4 Interface for Octave-Matlab NMF Algorithms

Accessing NMF Factors

Showing Arguments of 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.

Run NMF Methods and Generate a Report

plot,NMFfit,missing-method

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

Builds a Color Ramp from Compact Color Specification

Registering NMF Algorithms

show,NMFSeed-method

Show method for objects of class NMFSeed

show,NMFfitX1-method

Show method for objects of class NMFfitX1

show,NMFns-method

Show method for objects of class NMFns

Simple Progress Bar

nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS

NMFOffset-class

NMF Model - Nonnegative Matrix Factorization with Offset

algorithm,NMFList-method

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

Clustering Connectivity and Consensus Matrices

Dimension names for NMF objects

Running NMF algorithms

nmf_update.lsnmf

Multiplicative Updates for LS-NMF

Updating NMF Objects

Apply Function for NMF Objects

Randomizing Data

Flags a Color Palette Specification for Reversion

Comparing Results from Different NMF Runs

show,NMF-method

Show method for objects of class NMF

Factory Methods NMF Models

Class for Storing Heterogeneous NMF fits

nmf_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence

Structure for Storing the Best Fit Amongst Multiple NMF Runs

NMFStrategyIterative-class

Interface for Algorithms: Implementation for Iterative NMF Algorithms

Structure for Storing All Fits from Multiple NMF Runs

Golub ExpressionSet

Open a File Graphic Device

Fitted Matrix in NMF Models

nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence

Computational Setup Functions

Sub-setting NMF Objects

Base Class for to store Nonnegative Matrix Factorisation results

NMF Model - Standard model

NMF Model - Nonsmooth Nonnegative Matrix Factorization

Builds a Color Palette from Compact Color Specification

Dimension of NMF Objects

offset,NMFOffset-method

Offsets in NMF Models with Offset

Generate Break Intervals from Numeric Variables

Internal verbosity option

Purity and Entropy of a Clustering

Plotting Expression Profiles

Generating Random NMF Models

runtime.all,NMFfitXn-method

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

show,NMFfit-method

Show method for objects of class NMFfit

Testing NMF Objects

algorithm,NMFStrategyOctave-method

Returns the name of the Octave/Matlab function that implements the NMF algorithm -- as stored in slot algorithm.

Heatmaps of NMF Factors

Residual Sum of Squares and Explained Variance

show,NMFOffset-method

Show method for objects of class NMFOffset

Defunct Functions and Classes in the NMF Package

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

Generic Strategy Class

Error Checks in NMF Runs

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.

NMFStrategy-class

Virtual Interface for NMF Algorithms

Clustering and Prediction