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NMF (version 0.16.2)

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

0.16.2

License

GPL (>= 2)

Maintainer

Renaud Gaujoux

Last Published

March 27th, 2013

Functions in NMF (0.16.2)

nmf_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence

NMFStrategy-class

Virtual Interface for NMF Algorithms

Advanced Usage of the Package NMF

Structure for Storing All Fits from Multiple NMF Runs

Generic Strategy Class

Builds a Color Ramp from Compact Color Specification

Dimension names for NMF objects

registerDoBackend

Utilities and Extensions for Foreach Loops

Fitted Matrix in NMF Models

Apply Function for NMF Objects

Generating Random Matrices

Flags a Color Palette Specification for Reversion

show,NMF-method

Show method for objects of class NMF

Get/Set a Static Variable in NMF Algorithms

show,NMFfitX-method

Show method for objects of class NMFfitX

Utility Function in the NMF Package

Generate Break Intervals from Numeric Variables

Specific NMF Layer for Bioconductor

Concatenating NMF Models

Internal Routine for Fast Combinatorial Nonnegative Least-Squares

Fade Out the Upper Branches from a Dendrogram

nmf_update.euclidean_offset.h

NMF Multiplicative Update for NMF with Offset Models

Utilities for Parallel Computations

Clustering and Prediction

Base Class for to store Nonnegative Matrix Factorisation results

Annotated Heatmaps

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.

Extract Colour Palette Specification

Registry for NMF Algorithms

Generic Interface for Nonnegative Matrix Factorisation Models

NMFStrategyFunction-class

Interface for Single Function NMF Strategies

Error Checks in NMF Runs

Defunct Functions and Classes in the NMF Package

Builds a Color Palette from Compact Color Specification

Correlations in NMF Models

Comparing Results from Different NMF Runs

Dimension of NMF Objects

Updating Objects In Place

Updating NMF Objects

offset,NMFfit-method

Returns the offset from the fitted model.

Checking NMF Algorithm

Interface for NMF Seeding Methods

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.

Factory Method for NMFStrategy Objects

Factory Method for Multiple NMF Run Objects

NMFStrategyOctave-class

S4 Interface for Octave-Matlab NMF Algorithms

show,NMFOffset-method

Show method for objects of class NMFOffset

Structure for Storing the Best Fit Amongst Multiple NMF Runs

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 Model - Standard model

Stopping Criteria for NMF Iterative Strategies

show,NMFfitXn-method

Show method for objects of class NMFfitXn

nmf_update.lee_R

NMF Algorithm/Updates for Frobenius Norm

Algorithms and framework for Nonnegative Matrix Factorization (NMF).

NMFStrategyIterative-class

Interface for Algorithms: Implementation for Iterative NMF Algorithms

Distances and Objective Functions

nmfEstimateRank

Estimate Rank for NMF Models

NMFOffset-class

NMF Model - Nonnegative Matrix Factorization with Offset

Registering NMF Algorithms

Heatmaps of NMF Factors

Transforming from Mixed-sign to Nonnegative Data

Randomizing Data

algorithm,NMFStrategyOctave-method

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

Dispersion of a Matrix

Accessing NMF Factors

show,NMFList-method

Show method for objects of class NMFList

Annotation Tracks

show,NMFfitX1-method

Show method for objects of class NMFfitX1

NMF Model - Nonsmooth Nonnegative Matrix Factorization

show,NMFStrategyIterative-method

Show method for objects of class NMFStrategyIterative

Clustering Connectivity and Consensus Matrices

Hierarchical Clustering of a Consensus Matrix

Extending Annotation Vectors

Factory Methods NMF Models

nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence

Fast Combinatorial Nonnegative Least-Square

Seeding Strategies for NMF Algorithms

Residual Sum of Squares and Explained Variance

Plotting Expression Profiles

Residuals in NMF Models

Showing Arguments of NMF Algorithms

Computational Setup Functions

Class for Storing Heterogeneous NMF fits

nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS

Internal verbosity option

Fixed Terms in NMF Models

nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance

Simple Progress Bar

Simulating Datasets

Extracting Fitted Models

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms

Testing NMF Objects

Running NMF algorithms

Listing and Retrieving NMF Algorithms

Simple Parsing of Formula

offset,NMFOffset-method

Offsets in NMF Models with Offset

Generating Random NMF Models

Sub-setting NMF Objects

show,NMFSeed-method

Show method for objects of class NMFSeed

Transformation NMF Model Objects

show,NMFns-method

Show method for objects of class NMFns

Rescaling NMF Models

show,NMFfit-method

Show method for objects of class NMFfit

algorithmic-NMF

Generic Interface for Algorithms

Cluster Matrix Rows in Annotated Heatmaps

Cophenetic Correlation Coefficient

Deprecated Functions in the Package NMF

nmf_update.lsnmf

Multiplicative Updates for LS-NMF

grid.Call.graphics

Grid Internal Functions

Testing Equality of NMF Models

plot,NMFfit,missing-method

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

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

Purity and Entropy of a Clustering

Testing Compatibility of Algorithm and Models

Wrapping NMF Algorithms

Extracting RNG Data from NMF Objects

Base class that defines the interface for NMF seeding methods.

Assessing and Comparing NMF Models

Open a File Graphic Device

consensus,NMFfitX1-method

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

Golub ExpressionSet

consensus,NMFfitXn-method

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

NMF Package Specific Options

runtime.all,NMFfitXn-method

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

Feature Selection in NMF Models

Smoothing Matrix in Nonsmooth NMF Models

Fixed Terms in NMF Models