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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

10,088

Version

0.17

License

GPL (>= 2)

Maintainer

Renaud Gaujoux

Last Published

May 15th, 2013

Functions in NMF (0.17)

lverbose

Internal verbosity option
NMFfitX

Factory Method for Multiple NMF Run Objects
setNMFMethod

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.
compare-NMF

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.
options-NMF

NMF Package Specific Options
offset,NMFOffset-method

Offsets in NMF Models with Offset
nneg

Transforming from Mixed-sign to Nonnegative Data
consensushc

Hierarchical Clustering of a Consensus Matrix
dispersion

Dispersion of a Matrix
fcnnls

Fast Combinatorial Nonnegative Least-Square
nmfWrapper

Wrapping NMF Algorithms
methods-NMF

Registry for NMF Algorithms
rmatrix

Generating Random Matrices
.fcnnls

Internal Routine for Fast Combinatorial Nonnegative Least-Squares
nmfSeed

Seeding Strategies for NMF Algorithms
nmfEstimateRank

Estimate Rank for NMF Models
nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence
seed

Interface for NMF Seeding Methods
setupBackend

Computational Setup Functions
parallel-NMF

Utilities for Parallel Computations
nmfApply

Apply Function for NMF Objects
show,NMFfitXn-method

Show method for objects of class NMFfitXn
featureScore

Feature Selection in NMF Models
bterms<-

Fixed Terms in NMF Models
nmfObject

Updating NMF Objects
show,NMFns-method

Show method for objects of class NMFns
residuals

Residuals in NMF Models
runtime.all,NMFfitXn-method

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

Flags a Color Palette Specification for Reversion
NMFStrategy

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
gfile

Open a File Graphic Device
[,NMF-method

Sub-setting NMF Objects
smoothing

Smoothing Matrix in Nonsmooth NMF Models
profplot

Plotting Expression Profiles
scale.NMF

Rescaling NMF Models
nmfAlgorithm

Listing and Retrieving NMF Algorithms
nmfModel

Factory Methods NMF Models
nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS
rss

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
syntheticNMF

Simulating Datasets
txtProgressBar

Simple Progress Bar
sparseness

Sparseness
show,NMFfitX1-method

Show method for objects of class NMFfitX1
nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance
staticVar

Get/Set a Static Variable in NMF Algorithms
utils-NMF

Utility Function in the NMF Package
t.NMF

Transformation NMF Model Objects
nmf

Running NMF algorithms
is.nmf

Testing NMF Objects
c,NMF-method

Concatenating NMF Models
NMF-package

Algorithms and framework for Nonnegative Matrix Factorization (NMF).
fitted

Fitted Matrix in NMF Models
NMF-class

Generic Interface for Nonnegative Matrix Factorisation Models
NMFStrategy-class

Virtual Interface for NMF Algorithms
NMFStrategyFunction-class

Interface for Single Function NMF Strategies
nmfCheck

Checking NMF Algorithm
Strategy-class

Generic Strategy Class
getRNG1

Extracting RNG Data from NMF Objects
checkErrors

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.
NMFfitX-class

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
ccBreaks

Generate Break Intervals from Numeric Variables
algorithmic-NMF

Generic Interface for Algorithms
nmf_update.ns

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

NMF Model - Nonnegative Matrix Factorization with Offset
aheatmap

Annotated Heatmaps
.atrack

Annotation Tracks
cluster_mat

Cluster Matrix Rows in Annotated Heatmaps
parse_formula

Simple Parsing of Formula
basisnames

Dimension names for NMF objects
nbasis

Dimension of NMF Objects
canFit

Testing Compatibility of Algorithm and Models
nmf_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence
basiscor

Correlations in NMF Models
show,NMF-method

Show method for objects of class NMF
heatmap-NMF

Heatmaps of NMF Factors
randomize

Randomizing Data
basis

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-NMF

Advanced Usage of the Package NMF
pmax.inplace

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
bioc-NMF

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
rnmf

Generating Random NMF Models
NMFSeed-class

Base class that defines the interface for NMF seeding methods.
NMFfitXn-class

Structure for Storing All Fits from Multiple NMF Runs
summary

Assessing and Comparing NMF Models
ibterms

Fixed Terms in NMF Models
ccRamp

Builds a Color Ramp from Compact Color Specification
cophcor

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
cutdendro

Fade Out the Upper Branches from a Dendrogram
fit

Extracting Fitted Models
NMF-deprecated

Deprecated Functions in the Package NMF
match_atrack

Extending Annotation Vectors
nmf.equal

Testing Equality of NMF Models
NMFfit-class

Base Class for to store Nonnegative Matrix Factorisation results
purity

Purity and Entropy of a Clustering
grid.Call.graphics

Grid Internal Functions
NMFStop

Stopping Criteria for NMF Iterative Strategies
NMFStrategyOctave-class

S4 Interface for Octave-Matlab NMF Algorithms
connectivity

Clustering Connectivity and Consensus Matrices
NMFstd-class

NMF Model - Standard model
ccSpec

Extract Colour Palette Specification
registerDoBackend

Utilities and Extensions for Foreach Loops
NMFfitX1-class

Structure for Storing the Best Fit Amongst Multiple NMF Runs
esGolub

Golub ExpressionSet
nmfFormals

Showing Arguments of NMF Algorithms
ccPalette

Builds a Color Palette from Compact Color Specification
offset,NMFfit-method

Returns the offset from the fitted model.
predict

Clustering and Prediction
NMFns-class

NMF Model - Nonsmooth Nonnegative Matrix Factorization
NMF-defunct

Defunct Functions and Classes in the NMF Package
deviance

Distances and Objective Functions
NMFList-class

Class for Storing Heterogeneous NMF fits