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NMF (version 0.16.1)

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

0.16.1

License

GPL (>= 2)

Maintainer

Renaud Gaujoux

Last Published

March 27th, 2013

Functions in NMF (0.16.1)

Specific NMF Layer for Bioconductor

NMFStrategyFunction-class

Interface for Single Function NMF Strategies

Deprecated Functions in the Package NMF

Builds a Color Ramp from Compact Color Specification

Golub ExpressionSet

Extracting RNG Data from NMF Objects

Open a File Graphic Device

Updating Objects In Place

Algorithms and framework for Nonnegative Matrix Factorization (NMF).

Registry for NMF Algorithms

offset,NMFOffset-method

Offsets in NMF Models with Offset

NMFStrategyIterative-class

Interface for Algorithms: Implementation for Iterative NMF Algorithms

NMF Package Specific Options

Listing and Retrieving NMF Algorithms

Correlations in NMF Models

Annotated Heatmaps

NMF Model - Nonsmooth Nonnegative Matrix Factorization

algorithmic-NMF

Generic Interface for Algorithms

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms

Cluster Matrix Rows in Annotated Heatmaps

Fitted Matrix in NMF Models

Utilities for Parallel Computations

Extract Colour Palette Specification

Factory Method for NMFStrategy Objects

Base class that defines the interface for NMF seeding methods.

Defunct Functions and Classes in the NMF Package

Fade Out the Upper Branches from a Dendrogram

Residuals in NMF Models

Annotation Tracks

Hierarchical Clustering of a Consensus Matrix

Extending Annotation Vectors

nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS

Cophenetic Correlation Coefficient

Accessing NMF Factors

algorithm,NMFStrategyOctave-method

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

Fast Combinatorial Nonnegative Least-Square

Error Checks in NMF Runs

Testing Compatibility of Algorithm and Models

show,NMFfitX1-method

Show method for objects of class NMFfitX1

nmf_update.lee_R

NMF Algorithm/Updates for Frobenius Norm

nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance

Clustering and Prediction

grid.Call.graphics

Grid Internal Functions

Interface for NMF Seeding Methods

Purity and Entropy of a Clustering

Plotting Expression Profiles

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_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence

NMFOffset-class

NMF Model - Nonnegative Matrix Factorization with Offset

Comparing Results from Different NMF Runs

NMF Model - Standard model

Generate Break Intervals from Numeric Variables

Internal Routine for Fast Combinatorial Nonnegative Least-Squares

Wrapping NMF Algorithms

Testing NMF Objects

consensus,NMFfitXn-method

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

Extracting Fitted Models

Randomizing Data

plot,NMFfit,missing-method

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

Distances and Objective Functions

Dimension names for NMF objects

Residual Sum of Squares and Explained Variance

show,NMFStrategyIterative-method

Show method for objects of class NMFStrategyIterative

Factory Method for Multiple NMF Run Objects

nmfEstimateRank

Estimate Rank for NMF Models

nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence

Structure for Storing the Best Fit Amongst Multiple NMF Runs

Clustering Connectivity and Consensus Matrices

Class for Storing Heterogeneous NMF fits

Factory Methods NMF Models

Generic Strategy Class

nmf_update.lsnmf

Multiplicative Updates for LS-NMF

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.

show,NMFfitX-method

Show method for objects of class NMFfitX

Testing Equality of NMF Models

NMFSeed is a constructor method that instantiate NMFSeed objects.

show,NMF-method

Show method for objects of class NMF

Get/Set a Static Variable in NMF Algorithms

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.

show,NMFfit-method

Show method for objects of class NMFfit

Computational Setup Functions

Simple Progress Bar

Stopping Criteria for NMF Iterative Strategies

Updating NMF Objects

Utility Function in the NMF Package

registerDoBackend

Utilities and Extensions for Foreach Loops

show,NMFOffset-method

Show method for objects of class NMFOffset

Dimension of NMF Objects

Feature Selection in NMF Models

Sub-setting NMF Objects

Running NMF algorithms

show,NMFfitXn-method

Show method for objects of class NMFfitXn

Rescaling NMF Models

show,NMFSeed-method

Show method for objects of class NMFSeed

nmf_update.euclidean_offset.h

NMF Multiplicative Update for NMF with Offset Models

offset,NMFfit-method

Returns the offset from the fitted model.

Generating Random Matrices

Generating Random NMF Models

Flags a Color Palette Specification for Reversion

Transformation NMF Model Objects

NMFStrategyOctave-class

S4 Interface for Octave-Matlab NMF Algorithms

Generic Interface for Nonnegative Matrix Factorisation Models

Advanced Usage of the Package NMF

Builds a Color Palette from Compact Color Specification

Assessing and Comparing NMF Models

Internal verbosity option

Simple Parsing of Formula

runtime.all,NMFfitXn-method

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

show,NMFns-method

Show method for objects of class NMFns

Simulating Datasets

show,NMFList-method

Show method for objects of class NMFList

NMFStrategy-class

Virtual Interface for NMF Algorithms

Concatenating NMF Models

Base Class for to store Nonnegative Matrix Factorisation results

Structure for Storing All Fits from Multiple NMF Runs

consensus,NMFfitX1-method

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

Dispersion of a Matrix

Checking NMF Algorithm

Apply Function for NMF Objects

Showing Arguments of NMF Algorithms

Transforming from Mixed-sign to Nonnegative Data

Heatmaps of NMF Factors

Smoothing Matrix in Nonsmooth NMF Models

Fixed Terms in NMF Models

Fixed Terms in NMF Models

Registering NMF Algorithms

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