Algorithms and framework for Nonnegative Matrix Factorization (NMF).

Documentation for package ‘NMF’ version 0.5.06

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A B C D E F I M N O P R S misc

NMF-package

NMF Package Overview

-- A --

algorithm	Base Class for to store Nonnegative Matrix Factorisation results
algorithm-method	Class "NMFList" to Handle the Comparison of NMF Results
algorithm-method	Base Class for to store Nonnegative Matrix Factorisation results
algorithm-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
algorithm<-	Base Class for to store Nonnegative Matrix Factorisation results
algorithm<--method	Base Class for to store Nonnegative Matrix Factorisation results
as.NMFList	Comparing Results from Different NMF Runs
as.NMFList-method	Comparing Results from Different NMF Runs
as.NMFList-methods	Comparing Results from Different NMF Runs

-- B --

basis	Get/Set the matrix factors in a NMF model
basis-method	Base Class for to store Nonnegative Matrix Factorisation results
basis-method	Implement of the standard NMF model
basis-method	Get/Set the matrix factors in a NMF model
basis-methods	Get/Set the matrix factors in a NMF model
basis<-	Get/Set the matrix factors in a NMF model
basis<--method	Base Class for to store Nonnegative Matrix Factorisation results
basis<--method	Implement of the standard NMF model
basis<--method	Get/Set the matrix factors in a NMF model
basis<--methods	Get/Set the matrix factors in a NMF model
basisnames	Dimension names for NMF objects
basisnames-method	Dimension names for NMF objects
basisnames<-	Dimension names for NMF objects
basisnames<--method	Dimension names for NMF objects
basisnames<-.NMF	Dimension names for NMF objects

-- C --

coef	Get/Set the matrix factors in a NMF model
coef-method	Base Class for to store Nonnegative Matrix Factorisation results
coef-method	Implement of the standard NMF model
coef-method	Get/Set the matrix factors in a NMF model
coef<-	Get/Set the matrix factors in a NMF model
coef<--method	Base Class for to store Nonnegative Matrix Factorisation results
coef<--method	Implement of the standard NMF model
coef<--method	Get/Set the matrix factors in a NMF model
coef<--methods	Get/Set the matrix factors in a NMF model
coefficients	Get/Set the matrix factors in a NMF model
coefficients-method	Get/Set the matrix factors in a NMF model
coefficients<--method	Get/Set the matrix factors in a NMF model
compare	Comparing Results from Different NMF Runs
compare-method	Comparing Results from Different NMF Runs
compare-methods	Comparing Results from Different NMF Runs
connectivity	Class and Utility Methods for NMF objects
connectivity-method	Class and Utility Methods for NMF objects
connectivity-methods	Class and Utility Methods for NMF objects
consensus	Handling Results from Multiple NMF Runs
consensus-method	Interface Class for Nonnegative Matrix Factorisation Models
consensus-method	Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
consensus-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
consensus-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
consensus-methods	Handling Results from Multiple NMF Runs
cophcor	Handling Results from Multiple NMF Runs
cophcor-method	Handling Results from Multiple NMF Runs
cophcor-methods	Handling Results from Multiple NMF Runs

-- D --

dim-method	Interface Class for Nonnegative Matrix Factorisation Models
dim-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
dimnames-method	Dimension names for NMF objects
dimnames-NMF	Dimension names for NMF objects
dimnames<--method	Dimension names for NMF objects
dimnames<-.NMF	Dimension names for NMF objects
dispersion	Handling Results from Multiple NMF Runs
dispersion-method	Handling Results from Multiple NMF Runs
dispersion-methods	Handling Results from Multiple NMF Runs
distance	Interface Class for Nonnegative Matrix Factorisation Models
distance-method	Layer to use the NMF package within Bioconductor
distance-method	Interface Class for Nonnegative Matrix Factorisation Models
distance-method	Base Class for to store Nonnegative Matrix Factorisation results

-- E --

entropy	Class and Utility Methods for NMF objects
entropy-method	Class and Utility Methods for NMF objects
entropy-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
entropy-methods	Class and Utility Methods for NMF objects
esGolub	Golub ExpressionSet from Brunet et al. Paper
evar	Class and Utility Methods for NMF objects
evar-method	Class and Utility Methods for NMF objects
evar-methods	Class and Utility Methods for NMF objects
extractFeatures	Class and Utility Methods for NMF objects
extractFeatures-method	Class and Utility Methods for NMF objects

-- F --

fcnnls	Fast Combinatorial Non-Negative Least-Square
fcnnls-method	Fast Combinatorial Non-Negative Least-Square
featureNames	Interface Class for Nonnegative Matrix Factorisation Models
featureNames-method	Interface Class for Nonnegative Matrix Factorisation Models
featureNames-method	Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
featureNames<-	Interface Class for Nonnegative Matrix Factorisation Models
featureNames<--method	Interface Class for Nonnegative Matrix Factorisation Models
featureScore	Class and Utility Methods for NMF objects
featureScore-method	Class and Utility Methods for NMF objects
fit	Base Class for to store Nonnegative Matrix Factorisation results
fit-method	Base Class for to store Nonnegative Matrix Factorisation results
fit-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
fit-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
fit-method	Handling Results from Multiple NMF Runs
fit-methods	Base Class for to store Nonnegative Matrix Factorisation results
fit<-	Base Class for to store Nonnegative Matrix Factorisation results
fit<--method	Base Class for to store Nonnegative Matrix Factorisation results
fitted-method	Interface Class for Nonnegative Matrix Factorisation Models
fitted-method	Nonnegative Matrix Factorization with Offset
fitted-method	Base Class for to store Nonnegative Matrix Factorisation results
fitted-method	Nonsmooth Nonnegative Matrix Factorization
fitted-method	Implement of the standard NMF model

-- I --

initialize-method	Nonnegative Matrix Factorization with Offset
is.empty.nmf	Interface Class for Nonnegative Matrix Factorisation Models
is.empty.nmf-method	Interface Class for Nonnegative Matrix Factorisation Models
isNMFfit	Advanced usage of package NMF

-- M --

metagenes	Layer to use the NMF package within Bioconductor
metagenes-method	Layer to use the NMF package within Bioconductor
metagenes-methods	Layer to use the NMF package within Bioconductor
metagenes<-	Layer to use the NMF package within Bioconductor
metagenes<--method	Layer to use the NMF package within Bioconductor
metaHeatmap	Class and Utility Methods for NMF objects
metaHeatmap-method	Class and Utility Methods for NMF objects
metaHeatmap-method	Handling Results from Multiple NMF Runs
metaHeatmap-methods	Class and Utility Methods for NMF objects
metaprofiles	Layer to use the NMF package within Bioconductor
metaprofiles-method	Layer to use the NMF package within Bioconductor
metaprofiles-methods	Layer to use the NMF package within Bioconductor
metaprofiles<-	Layer to use the NMF package within Bioconductor
metaprofiles<--method	Layer to use the NMF package within Bioconductor
modelname	Interface Class for Nonnegative Matrix Factorisation Models
modelname-method	Interface Class for Nonnegative Matrix Factorisation Models
modelname-method	Base Class for to store Nonnegative Matrix Factorisation results

-- N --

nbasis	Interface Class for Nonnegative Matrix Factorisation Models
nbasis-method	Interface Class for Nonnegative Matrix Factorisation Models
niter	Base Class for to store Nonnegative Matrix Factorisation results
niter-method	Base Class for to store Nonnegative Matrix Factorisation results
niter-methods	Base Class for to store Nonnegative Matrix Factorisation results
niter<--method	Base Class for to store Nonnegative Matrix Factorisation results
nmeta	Layer to use the NMF package within Bioconductor
nmeta-method	Layer to use the NMF package within Bioconductor
nmeta-methods	Layer to use the NMF package within Bioconductor
NMF	NMF Package Overview
nmf	Main Interface to run NMF algorithms
NMF Algorithms	Main Interface to run NMF algorithms
NMF-advanced	Advanced usage of package NMF
NMF-bioc	Layer to use the NMF package within Bioconductor
NMF-class	Interface Class for Nonnegative Matrix Factorisation Models
nmf-compare	Comparing Results from Different NMF Runs
nmf-method	Main Interface to run NMF algorithms
nmf-methods	Main Interface to run NMF algorithms
nmf-multiple	Handling Results from Multiple NMF Runs
NMF-options	Package Specific Option Management
NMF-utils	Class and Utility Methods for NMF objects
nmf.getOption	Package Specific Option Management
nmf.options	Package Specific Option Management
nmf.options.reset	Package Specific Option Management
nmf.options.runtime	Package Specific Option Management
nmfApply	Class and Utility Methods for NMF objects
nmfApply-method	Class and Utility Methods for NMF objects
nmfEstimateRank	Estimate optimal rank for Nonnegative Matrix Factorization (NMF) models
NMFfit-class	Base Class for to store Nonnegative Matrix Factorisation results
NMFfitX-class	Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
NMFfitX1-class	Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
NMFfitXn-class	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
NMFList-class	Class "NMFList" to Handle the Comparison of NMF Results
nmfModel	Factory Method for NMF Models
nmfModel-method	Factory Method for NMF Models
nmfModel-methods	Factory Method for NMF Models
NMFns-class	Nonsmooth Nonnegative Matrix Factorization
NMFOffset-class	Nonnegative Matrix Factorization with Offset
NMFSet-class	Deprecated Class to store results from multiple runs of NMF algorithms
NMFstd-class	Implement of the standard NMF model
nrun	Handling Results from Multiple NMF Runs
nrun-method	Base Class for to store Nonnegative Matrix Factorisation results
nrun-method	Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
nrun-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
nrun-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
nrun-methods	Handling Results from Multiple NMF Runs

-- O --

objective	Base Class for to store Nonnegative Matrix Factorisation results
objective-method	Base Class for to store Nonnegative Matrix Factorisation results
objective<-	Base Class for to store Nonnegative Matrix Factorisation results
objective<--method	Base Class for to store Nonnegative Matrix Factorisation results
offset-method	Nonnegative Matrix Factorization with Offset

-- P --

plot-method	Class and Utility Methods for NMF objects
plot-method	Comparing Results from Different NMF Runs
plot.NMF.rank	Estimate optimal rank for Nonnegative Matrix Factorization (NMF) models
predict	Class and Utility Methods for NMF objects
predict-method	Class and Utility Methods for NMF objects
predict-method	Handling Results from Multiple NMF Runs
predict-methods	Class and Utility Methods for NMF objects
purity	Class and Utility Methods for NMF objects
purity-method	Class and Utility Methods for NMF objects
purity-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
purity-methods	Class and Utility Methods for NMF objects

-- R --

randomize	Class and Utility Methods for NMF objects
residuals	Class and Utility Methods for NMF objects
residuals-method	Class and Utility Methods for NMF objects
residuals-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
residuals<-	Base Class for to store Nonnegative Matrix Factorisation results
residuals<--method	Base Class for to store Nonnegative Matrix Factorisation results
residuals<--methods	Base Class for to store Nonnegative Matrix Factorisation results
rmatrix	Generates a Random Matrix Using Any Given Distribution Function
rnmf	Interface Class for Nonnegative Matrix Factorisation Models
rnmf-method	Interface Class for Nonnegative Matrix Factorisation Models
rnmf-method	Nonnegative Matrix Factorization with Offset
rnmf-methods	Interface Class for Nonnegative Matrix Factorisation Models
rss	Class and Utility Methods for NMF objects
rss-method	Class and Utility Methods for NMF objects
runtime	Base Class for to store Nonnegative Matrix Factorisation results
runtime-method	Class "NMFList" to Handle the Comparison of NMF Results
runtime-method	Base Class for to store Nonnegative Matrix Factorisation results
runtime.all	Handling Results from Multiple NMF Runs
runtime.all-method	Base Class for to store Nonnegative Matrix Factorisation results
runtime.all-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
runtime.all-method	Handling Results from Multiple NMF Runs
runtime.all-methods	Handling Results from Multiple NMF Runs

-- S --

sampleNames	Interface Class for Nonnegative Matrix Factorisation Models
sampleNames-method	Interface Class for Nonnegative Matrix Factorisation Models
sampleNames-method	Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
sampleNames<-	Interface Class for Nonnegative Matrix Factorisation Models
sampleNames<--method	Interface Class for Nonnegative Matrix Factorisation Models
seed	Main Interface to run NMF algorithms
seeding	Base Class for to store Nonnegative Matrix Factorisation results
seeding-method	Base Class for to store Nonnegative Matrix Factorisation results
seeding-methods	Base Class for to store Nonnegative Matrix Factorisation results
seeding<-	Base Class for to store Nonnegative Matrix Factorisation results
seeding<--method	Base Class for to store Nonnegative Matrix Factorisation results
seqtime	Handling Results from Multiple NMF Runs
seqtime-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
seqtime-methods	Handling Results from Multiple NMF Runs
show-method	Interface Class for Nonnegative Matrix Factorisation Models
show-method	Class "NMFList" to Handle the Comparison of NMF Results
show-method	Nonnegative Matrix Factorization with Offset
show-method	Base Class for to store Nonnegative Matrix Factorisation results
show-method	Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
show-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
show-method	Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
show-method	Nonsmooth Nonnegative Matrix Factorization
smoothing	Nonsmooth Nonnegative Matrix Factorization
smoothing-method	Nonsmooth Nonnegative Matrix Factorization
smoothing-methods	Nonsmooth Nonnegative Matrix Factorization
sparseness	Class and Utility Methods for NMF objects
sparseness-method	Class and Utility Methods for NMF objects
sparseness-methods	Class and Utility Methods for NMF objects
subset-NMF	Subset method for objects of class NMF
summary-method	Interface Class for Nonnegative Matrix Factorisation Models
summary-method	Base Class for to store Nonnegative Matrix Factorisation results
summary-method	Comparing Results from Different NMF Runs
summary-method	Handling Results from Multiple NMF Runs
syntheticNMF	Class and Utility Methods for NMF objects

-- misc --

$	Base Class for to store Nonnegative Matrix Factorisation results
$-method	Base Class for to store Nonnegative Matrix Factorisation results
$<-	Base Class for to store Nonnegative Matrix Factorisation results
$<--method	Base Class for to store Nonnegative Matrix Factorisation results
[-method	Subset method for objects of class NMF