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NMF (version 0.2.2)

Framework for Nonnegative Matrix Factorization (NMF) algorithms.

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 and develop new algorithms.

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Version

Install

install.packages('NMF')

Monthly Downloads

17,215

Version

0.2.2

License

GPL (>= 2)

Maintainer

Renaud Gaujoux

Last Published

November 26th, 2009

Functions in NMF (0.2.2)

NMF-bioc

Layer to use the NMF package within Bioconductor
NMFOffset-class

Nonnegative Matrix Factorization with Offset
esGolub

Golub ExpressionSet from Brunet et al. Paper
Internals

Undocumented or Internal methods and functions for package NMF
nmf-methods

Main Interface to run NMF algorithms
NMFSet-class

Class to store results from multiple runs of NMF algorithms
nmfEstimateRank

Estimate optimal rank for Nonnegative Matrix Factorization (NMF) models
NMF-utils

Class and Utility Methods for NMF objects
NMFstd-class

Implement of the standard NMF model
NMFns-class

Nonsmooth Nonnegative Matrix Factorization
NMFfit-class

Base Class for to store Nonnegative Matrix Factorisation results
advanced

Advanced usage of package NMF
NMF-class

Interface class for Nonnegative Matrix Factorisation models
basis-methods

Extract/Set the matrix of basis vectors from a NMF model
NMFStrategyFunction-class

Interface for Single Function NMF Strategies
NMF-package

NMF Package Overview
deviance

Distances and Objective Functions
ccRamp

Builds a Color Ramp from Compact Color Specification
pmax.inplace

Updating Objects In Place
NMF-deprecated

Deprecated functions in NMF package
consensushc

Hierarchical Clustering of a Consensus Matrix
algorithm,NMFList-method

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

Open a File Graphic Device
connectivity

Clustering Connectivity and Consensus Matrices
cutdendro

Fade Out the Upper Branches from a Dendrogram
ibterms

Fixed Terms in NMF Models
nmf_update.lsnmf

Multiplicative Updates for LS-NMF
rnmf

Generating Random NMF Models
bioc-NMF

Specific NMF Layer for Bioconductor
advanced-NMF

Advanced Usage of the Package NMF
nmfFormals

Showing Arguments of NMF Algorithms
NMFfitX

Factory Method for Multiple NMF Run Objects
parse_formula

Simple Parsing of Formula
silhouette.NMF

Silhouette of NMF Clustering
checkErrors

Error Checks in NMF Runs
Strategy-class

Generic Strategy Class
bterms<-

Fixed Terms in NMF Models
NMFfitX-class

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
NMFStrategyOctave-class

S4 Interface for Octave-Matlab NMF Algorithms
purity

Purity and Entropy of a Clustering
nmfApply

Apply Function for NMF Objects
cophcor

Cophenetic Correlation Coefficient
show,NMFList-method

Show method for objects of class NMFList
canFit

Testing Compatibility of Algorithm and Models
consensus,NMFfitXn-method

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

Show method for objects of class NMFns
nmfWrapper

Wrapping NMF Algorithms
nmfObject

Updating NMF Objects
setupBackend

Computational Setup Functions
nmf.equal

Testing Equality of NMF Models
profplot

Plotting Expression Profiles
consensus,NMFfitX1-method

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

NMF Algorithm/Updates for Frobenius Norm
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.
basisnames

Dimension names for NMF objects
c,NMF-method

Concatenating NMF Models
rss

Residual Sum of Squares and Explained Variance
nbasis

Dimension of NMF Objects
nmfModel

Factory Methods NMF Models
show,NMFSeed-method

Show method for objects of class NMFSeed
is.nmf

Testing NMF Objects
NMFList-class

Class for Storing Heterogeneous NMF fits
basis

Accessing NMF Factors
txtProgressBar

Simple Progress Bar
fcnnls

Fast Combinatorial Nonnegative Least-Square
ccPalette

Builds a Color Palette from Compact Color Specification
t.NMF

Transformation NMF Model Objects
NMF-defunct

Defunct Functions and Classes in the NMF Package
show,NMFfit-method

Show method for objects of class NMFfit
show,NMFStrategyIterative-method

Show method for objects of class NMFStrategyIterative
cluster_mat

Cluster Matrix Rows in Annotated Heatmaps
dispersion

Dispersion of a Matrix
NMFSeed-class

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

Heatmaps of NMF Factors
tryViewport

Internal Grid Extension
ccSpec

Extract Colour Palette Specification
algorithm,NMFStrategyOctave-method

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

Returns the offset from the fitted model.
match_atrack

Extending Annotation Vectors
smoothing

Smoothing Matrix in Nonsmooth NMF Models
parallel-NMF

Utilities for Parallel Computations
setNMFMethod

Registering NMF Algorithms
lverbose

Internal verbosity option
registerDoBackend

Utilities and Extensions for Foreach Loops
summary

Assessing and Comparing NMF Models
nmf_update.ns

NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
runtime.all,NMFfitXn-method

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

Registry for NMF Algorithms
algorithmic-NMF

Generic Interface for Algorithms
nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS
offset,NMFOffset-method

Offsets in NMF Models with Offset
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.
utils-NMF

Utility Function in the NMF Package
show,NMFfitX-method

Show method for objects of class NMFfitX
rmatrix

Generating Random Matrices
basiscor

Correlations in NMF Models
residuals

Residuals in NMF Models
featureScore

Feature Selection in NMF Models
nmf_update.euclidean_offset.h

NMF Multiplicative Update for NMF with Offset Models
NMFStrategy

Factory Method for NMFStrategy Objects
[,NMF-method

Sub-setting NMF Objects
syntheticNMF

Simulating Datasets
nmfCheck

Checking NMF Algorithm
nneg

Transforming from Mixed-sign to Nonnegative Data
NMFfitX1-class

Structure for Storing the Best Fit Amongst Multiple NMF Runs
nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance
nmfSeed

Seeding Strategies for NMF Algorithms
aheatmap

Annotated Heatmaps
fit

Extracting Fitted Models
.fcnnls

Internal Routine for Fast Combinatorial Nonnegative Least-Squares
getRNG1

Extracting RNG Data from NMF Objects
nmf

Running NMF algorithms
NMFfitXn-class

Structure for Storing All Fits from Multiple NMF Runs
compare-NMF

Comparing Results from Different NMF Runs
options-NMF

NMF Package Specific Options
plot,NMFfit,missing-method

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

Interface for Algorithms: Implementation for Iterative NMF Algorithms
ccBreaks

Generate Break Intervals from Numeric Variables
nmfAlgorithm

Listing and Retrieving NMF Algorithms
fitted

Fitted Matrix in NMF Models
NMFStop

Stopping Criteria for NMF Iterative Strategies
revPalette

Flags a Color Palette Specification for Reversion
staticVar

Get/Set a Static Variable in NMF Algorithms
show,NMFfitX1-method

Show method for objects of class NMFfitX1
sparseness

Sparseness
show,NMF-method

Show method for objects of class NMF
show,NMFfitXn-method

Show method for objects of class NMFfitXn
nmfReport

Run NMF Methods and Generate a Report
NMFStrategy-class

Virtual Interface for NMF Algorithms
nmf_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence
seed

Interface for NMF Seeding Methods
.atrack

Annotation Tracks
predict

Clustering and Prediction
nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence
randomize

Randomizing Data
scale.NMF

Rescaling NMF Models
show,NMFOffset-method

Show method for objects of class NMFOffset