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NMF (version 0.20.2)

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

9,744

Version

0.20.2

License

GPL (>= 2)

Maintainer

Renaud Gaujoux

Last Published

March 9th, 2014

Functions in NMF (0.20.2)

NMFfitX

Factory Method for Multiple NMF Run Objects
NMFStrategyFunction-class

Interface for Single Function NMF Strategies
getRNG1

Extracting RNG Data from NMF Objects
consensushc

Hierarchical Clustering of a Consensus Matrix
esGolub

Golub ExpressionSet
gfile

Open a File Graphic Device
tryViewport

Internal Grid Extension
registerDoBackend

Utilities and Extensions for Foreach Loops
nmfEstimateRank

Estimate Rank for NMF Models
plot,NMFfit,missing-method

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

Flags a Color Palette Specification for Reversion
sparseness

Sparseness
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.
is.nmf

Testing NMF Objects
NMF-defunct

Defunct Functions and Classes in the NMF Package
NMFOffset-class

NMF Model - Nonnegative Matrix Factorization with Offset
NMFfitXn-class

Structure for Storing All Fits from 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.
ccRamp

Builds a Color Ramp from Compact Color Specification
Strategy-class

Generic Strategy Class
ccPalette

Builds a Color Palette from Compact Color Specification
NMFStrategy

Factory Method for NMFStrategy Objects
deviance

Distances and Objective Functions
lverbose

Internal verbosity option
dispersion

Dispersion of a Matrix
cluster_mat

Cluster Matrix Rows in Annotated Heatmaps
NMFList-class

Class for Storing Heterogeneous NMF fits
bioc-NMF

Specific NMF Layer for Bioconductor
consensus,NMFfitXn-method

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

Showing Arguments of NMF Algorithms
nmfCheck

Checking NMF Algorithm
silhouette.NMF

Silhouette of NMF Clustering
show,NMFStrategyIterative-method

Show method for objects of class NMFStrategyIterative
[,NMF-method

Sub-setting NMF Objects
fcnnls

Fast Combinatorial Nonnegative Least-Square
basisnames

Dimension names for NMF objects
parallel-NMF

Utilities for Parallel Computations
rnmf

Generating Random NMF Models
setNMFMethod

Registering NMF Algorithms
show,NMFfitXn-method

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

Show method for objects of class NMFOffset
NMFStop

Stopping Criteria for NMF Iterative Strategies
show,NMFSeed-method

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

Show method for objects of class NMF
nmfObject

Updating NMF Objects
offset,NMFfit-method

Returns the offset from the fitted model.
nmfApply

Apply Function for NMF Objects
profplot

Plotting Expression Profiles
residuals

Residuals in NMF Models
seed

Interface for NMF Seeding Methods
bterms<-

Fixed Terms in NMF Models
nmfSeed

Seeding Strategies for NMF Algorithms
NMF-deprecated

Deprecated Functions in the Package NMF
NMFfitX-class

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
.atrack

Annotation Tracks
canFit

Testing Compatibility of Algorithm and Models
nmf.equal

Testing Equality of NMF Models
basis

Accessing NMF Factors
nbasis

Dimension of NMF Objects
nmfModel

Factory Methods NMF Models
purity

Purity and Entropy of a Clustering
options-NMF

NMF Package Specific Options
nmf_update.KL.h

NMF Multiplicative Updates for Kullback-Leibler Divergence
show,NMFfit-method

Show method for objects of class NMFfit
nmf_update.brunet_R

NMF Algorithm/Updates for Kullback-Leibler Divergence
NMFSeed-class

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

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

Assessing and Comparing NMF Models
consensus,NMFfitX1-method

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

Cophenetic Correlation Coefficient
nmfAlgorithm

Listing and Retrieving NMF Algorithms
aheatmap

Annotated Heatmaps
show,NMFns-method

Show method for objects of class NMFns
syntheticNMF

Simulating Datasets
NMF-class

Generic Interface for Nonnegative Matrix Factorisation Models
NMFStrategy-class

Virtual Interface for NMF Algorithms
heatmap-NMF

Heatmaps of NMF Factors
NMFStrategyIterative-class

Interface for Algorithms: Implementation for Iterative NMF Algorithms
ccBreaks

Generate Break Intervals from Numeric Variables
nmfAlgorithm.SNMF_R

NMF Algorithm - Sparse NMF via Alternating NNLS
connectivity

Clustering Connectivity and Consensus Matrices
NMFfitX1-class

Structure for Storing the Best Fit Amongst Multiple NMF Runs
basiscor

Correlations in NMF Models
checkErrors

Error Checks in NMF Runs
fitted

Fitted Matrix in NMF Models
fit

Extracting Fitted Models
c,NMF-method

Concatenating NMF Models
NMFns-class

NMF Model - Nonsmooth Nonnegative Matrix Factorization
algorithm,NMFStrategyOctave-method

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

Base Class for to store Nonnegative Matrix Factorisation results
NMFstd-class

NMF Model - Standard model
advanced-NMF

Advanced Usage of the Package NMF
algorithmic-NMF

Generic Interface for Algorithms
cutdendro

Fade Out the Upper Branches from a Dendrogram
.fcnnls

Internal Routine for Fast Combinatorial Nonnegative Least-Squares
nmfReport

Run NMF Methods and Generate a Report
ccSpec

Extract Colour Palette Specification
nmf

Running NMF algorithms
scale.NMF

Rescaling NMF Models
nmf_update.lsnmf

Multiplicative Updates for LS-NMF
compare-NMF

Comparing Results from Different NMF Runs
offset,NMFOffset-method

Offsets in NMF Models with Offset
utils-NMF

Utility Function in the NMF Package
parse_formula

Simple Parsing of Formula
rss

Residual Sum of Squares and Explained Variance
nmf_update.ns

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

Fixed Terms in NMF Models
nmf_update.euclidean_offset.h

NMF Multiplicative Update for NMF with Offset Models
runtime.all,NMFfitXn-method

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

Generating Random Matrices
methods-NMF

Registry for NMF Algorithms
randomize

Randomizing Data
setupBackend

Computational Setup Functions
featureScore

Feature Selection in NMF Models
show,NMFfitX-method

Show method for objects of class NMFfitX
t.NMF

Transformation NMF Model Objects
staticVar

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,NMFList-method

Show method for objects of class NMFList
smoothing

Smoothing Matrix in Nonsmooth NMF Models
nmf_update.euclidean.h

NMF Multiplicative Updates for Euclidean Distance
nmf_update.lee_R

NMF Algorithm/Updates for Frobenius Norm
NMFStrategyOctave-class

S4 Interface for Octave-Matlab NMF Algorithms
pmax.inplace

Updating Objects In Place
match_atrack

Extending Annotation Vectors
show,NMFfitX1-method

Show method for objects of class NMFfitX1
nneg

Transforming from Mixed-sign to Nonnegative Data
predict

Clustering and Prediction
nmfWrapper

Wrapping NMF Algorithms
txtProgressBar

Simple Progress Bar