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NMF (version 0.17)

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

0.17

License

GPL (>= 2)

Maintainer

Renaud Gaujoux

Last Published

May 15th, 2013

Functions in NMF (0.17)

Internal verbosity option

Factory Method for Multiple NMF Run Objects

Registering NMF Algorithms

consensus,NMFfitXn-method

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

plot,NMFfit,missing-method

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

Comparing Results from Different NMF Runs

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.

NMF Package Specific Options

offset,NMFOffset-method

Offsets in NMF Models with Offset

Transforming from Mixed-sign to Nonnegative Data

Hierarchical Clustering of a Consensus Matrix

Dispersion of a Matrix

Fast Combinatorial Nonnegative Least-Square

Wrapping NMF Algorithms

Registry for NMF Algorithms

Generating Random Matrices

Internal Routine for Fast Combinatorial Nonnegative Least-Squares

Seeding Strategies for NMF Algorithms

nmfEstimateRank

Estimate Rank for NMF Models

nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence

Interface for NMF Seeding Methods

Computational Setup Functions

Utilities for Parallel Computations

Apply Function for NMF Objects

show,NMFfitXn-method

Show method for objects of class NMFfitXn

Feature Selection in NMF Models

Fixed Terms in NMF Models

Updating NMF Objects

show,NMFns-method

Show method for objects of class NMFns

Residuals in NMF Models

runtime.all,NMFfitXn-method

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

Flags a Color Palette Specification for Reversion

Factory Method for NMFStrategy Objects

show,NMFSeed-method

Show method for objects of class NMFSeed

nmf_update.euclidean_offset.h

NMF Multiplicative Update for NMF with Offset Models

Open a File Graphic Device

Sub-setting NMF Objects

Smoothing Matrix in Nonsmooth NMF Models

Plotting Expression Profiles

Rescaling NMF Models

Listing and Retrieving NMF Algorithms

Factory Methods NMF Models

nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS

Residual Sum of Squares and Explained Variance

show,NMFfit-method

Show method for objects of class NMFfit

show,NMFStrategyIterative-method

Show method for objects of class NMFStrategyIterative

Simulating Datasets

Simple Progress Bar

show,NMFfitX1-method

Show method for objects of class NMFfitX1

nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance

Get/Set a Static Variable in NMF Algorithms

Utility Function in the NMF Package

Transformation NMF Model Objects

Running NMF algorithms

Testing NMF Objects

Concatenating NMF Models

Algorithms and framework for Nonnegative Matrix Factorization (NMF).

Fitted Matrix in NMF Models

Generic Interface for Nonnegative Matrix Factorisation Models

NMFStrategy-class

Virtual Interface for NMF Algorithms

NMFStrategyFunction-class

Interface for Single Function NMF Strategies

Checking NMF Algorithm

Generic Strategy Class

Extracting RNG Data from NMF Objects

Error Checks in NMF Runs

consensus,NMFfitX1-method

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

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms

Generate Break Intervals from Numeric Variables

algorithmic-NMF

Generic Interface for Algorithms

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

NMFOffset-class

NMF Model - Nonnegative Matrix Factorization with Offset

Annotated Heatmaps

Annotation Tracks

Cluster Matrix Rows in Annotated Heatmaps

Simple Parsing of Formula

Dimension names for NMF objects

Dimension of NMF Objects

Testing Compatibility of Algorithm and Models

nmf_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence

Correlations in NMF Models

show,NMF-method

Show method for objects of class NMF

Heatmaps of NMF Factors

Randomizing Data

Accessing NMF Factors

algorithm,NMFList-method

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

Advanced Usage of the Package NMF

Updating Objects In Place

show,NMFOffset-method

Show method for objects of class NMFOffset

show,NMFList-method

Show method for objects of class NMFList

algorithm,NMFStrategyOctave-method

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

show,NMFfitX-method

Show method for objects of class NMFfitX

Specific NMF Layer for Bioconductor

nmf_update.lee_R

NMF Algorithm/Updates for Frobenius Norm

NMFStrategyIterative-class

Interface for Algorithms: Implementation for Iterative NMF Algorithms

Generating Random NMF Models

Base class that defines the interface for NMF seeding methods.

Structure for Storing All Fits from Multiple NMF Runs

Assessing and Comparing NMF Models

Fixed Terms in NMF Models

Builds a Color Ramp from Compact Color Specification

Cophenetic Correlation Coefficient

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.

nmf_update.lsnmf

Multiplicative Updates for LS-NMF

Fade Out the Upper Branches from a Dendrogram

Extracting Fitted Models

Deprecated Functions in the Package NMF

Extending Annotation Vectors

Testing Equality of NMF Models

Base Class for to store Nonnegative Matrix Factorisation results

Purity and Entropy of a Clustering

grid.Call.graphics

Grid Internal Functions

Stopping Criteria for NMF Iterative Strategies

NMFStrategyOctave-class

S4 Interface for Octave-Matlab NMF Algorithms

Clustering Connectivity and Consensus Matrices

NMF Model - Standard model

Extract Colour Palette Specification

registerDoBackend

Utilities and Extensions for Foreach Loops

Structure for Storing the Best Fit Amongst Multiple NMF Runs

Golub ExpressionSet

Showing Arguments of NMF Algorithms

Builds a Color Palette from Compact Color Specification

offset,NMFfit-method

Returns the offset from the fitted model.

Clustering and Prediction

NMF Model - Nonsmooth Nonnegative Matrix Factorization

Defunct Functions and Classes in the NMF Package

Distances and Objective Functions

Class for Storing Heterogeneous NMF fits