Algorithms and framework for Nonnegative Matrix Factorization (NMF).


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Documentation for package ‘NMF’ version 0.2.4

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

-- --

NMF-package NMF Package Overview

-- A --

algorithm Base Class for to store Nonnegative Matrix Factorisation results
algorithm,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
algorithm,NMFSet-method Class to store results from multiple runs of NMF algorithms
algorithm,NMFStrategyFunction-method Undocumented or Internal methods and functions for package NMF
algorithm<- Base Class for to store Nonnegative Matrix Factorisation results
algorithm<-,NMFfit,ANY-method Base Class for to store Nonnegative Matrix Factorisation results
algorithm<-,NMFStrategyFunction,character-method Undocumented or Internal methods and functions for package NMF
algorithm<-,NMFStrategyFunction,function-method Undocumented or Internal methods and functions for package NMF

-- B --

basis Extract/Set the matrix of basis vectors from a NMF model
basis,NMF-method Extract/Set the matrix of basis vectors from a NMF model
basis,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
basis,NMFstd-method Implement of the standard NMF model
basis-methods Extract/Set the matrix of basis vectors from a NMF model
basis<- Extract/Set the matrix of basis vectors from a NMF model
basis<-,NMF,matrix-method Extract/Set the matrix of basis vectors from a NMF model
basis<-,NMFfit,matrix-method Base Class for to store Nonnegative Matrix Factorisation results
basis<-,NMFstd,matrix-method Implement of the standard NMF model
basis<--methods Extract/Set the matrix of basis vectors from a NMF model

-- C --

clusters Deprecated functions in NMF package
clusters,matrix-method Deprecated functions in NMF package
clusters,NMF-method Deprecated functions in NMF package
clusters-methods Deprecated functions in NMF package
coef Extract/Set the matrix of basis vectors from a NMF model
coef,NMF-method Extract/Set the matrix of basis vectors from a NMF model
coef,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
coef,NMFstd-method Implement of the standard NMF model
coef<- Extract/Set the matrix of basis vectors from a NMF model
coef<-,NMF,matrix-method Extract/Set the matrix of basis vectors from a NMF model
coef<-,NMFfit,matrix-method Base Class for to store Nonnegative Matrix Factorisation results
coef<-,NMFstd,matrix-method Implement of the standard NMF model
coef<--methods Extract/Set the matrix of basis vectors from a NMF model
coefficients Extract/Set the matrix of basis vectors from a NMF model
coefficients,NMF-method Extract/Set the matrix of basis vectors from a NMF model
coefficients<-,NMF,matrix-method Extract/Set the matrix of basis vectors from a NMF model
compare Class to store results from multiple runs of NMF algorithms
compare,list-method Class to store results from multiple runs of NMF algorithms
compare,NMFSet-method Class to store results from multiple runs of NMF algorithms
connectivity Class and Utility Methods for NMF objects
connectivity,NMF-method Class and Utility Methods for NMF objects
connectivity,NMFSet-method Class to store results from multiple runs of NMF algorithms
connectivity-methods Class and Utility Methods for NMF objects
cophcor Class and Utility Methods for NMF objects
cophcor,matrix-method Class and Utility Methods for NMF objects
cophcor,NMFSet-method Class to store results from multiple runs of NMF algorithms
cophcor-methods Class and Utility Methods for NMF objects

-- D --

dim,NMF-method Interface class for Nonnegative Matrix Factorisation models
dispersion Class and Utility Methods for NMF objects
dispersion,matrix-method Class and Utility Methods for NMF objects
dispersion,NMFSet-method Class to store results from multiple runs of NMF algorithms
dispersion-methods Class and Utility Methods for NMF objects
distance Interface class for Nonnegative Matrix Factorisation models
distance,matrix,NMF-method Interface class for Nonnegative Matrix Factorisation models
distance,matrix,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results

-- E --

entropy Class and Utility Methods for NMF objects
entropy,factor,factor-method Class and Utility Methods for NMF objects
entropy,NMF,factor-method Class and Utility Methods for NMF objects
entropy,NMF,factor-method Class and Utility Methods for NMF objects
entropy,NMFSet,ANY-method Class to store results from multiple runs of NMF algorithms
entropy,table,missing-method Class and Utility Methods for NMF objects
entropy-methods Class and Utility Methods for NMF objects
errorPlot Base Class for to store Nonnegative Matrix Factorisation results
errorPlot,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
errorPlot,NMFSet-method Class to store results from multiple runs of NMF algorithms
esGolub Golub ExpressionSet from Brunet et al. Paper
extra Base Class for to store Nonnegative Matrix Factorisation results
extra,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
extra-methods Base Class for to store Nonnegative Matrix Factorisation results
extractFeatures Class and Utility Methods for NMF objects
extractFeatures,NMF-method Class and Utility Methods for NMF objects

-- F --

featureNames Interface class for Nonnegative Matrix Factorisation models
featureNames,NMF-method Interface class for Nonnegative Matrix Factorisation models
featureNames,NMFSet-method Class to store results from multiple runs of NMF algorithms
featureNames<- Interface class for Nonnegative Matrix Factorisation models
featureNames<-,NMF-method Interface class for Nonnegative Matrix Factorisation models
featureScore Class and Utility Methods for NMF objects
featureScore,matrix-method Class and Utility Methods for NMF objects
featureScore,NMF-method Class and Utility Methods for NMF objects
fit Base Class for to store Nonnegative Matrix Factorisation results
fit,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
fit,NMFSet-method Class to store results from multiple runs of NMF algorithms
fit-methods Base Class for to store Nonnegative Matrix Factorisation results
fit<- Base Class for to store Nonnegative Matrix Factorisation results
fit<-,NMFfit,NMF-method Base Class for to store Nonnegative Matrix Factorisation results
fitted,NMF-method Interface class for Nonnegative Matrix Factorisation models
fitted,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
fitted,NMFns-method Nonsmooth Nonnegative Matrix Factorization
fitted,NMFOffset-method Nonnegative Matrix Factorization with Offset
fitted,NMFstd-method Implement of the standard NMF model

-- I --

initialize,NMFOffset-method Nonnegative Matrix Factorization with Offset
is.empty.nmf Interface class for Nonnegative Matrix Factorisation models
is.empty.nmf,NMF-method Interface class for Nonnegative Matrix Factorisation models

-- J --

join Class to store results from multiple runs of NMF algorithms
join,list-method Class to store results from multiple runs of NMF algorithms

-- M --

metagenes Layer to use the NMF package within Bioconductor
metagenes,NMF-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<-,NMF,matrix-method Layer to use the NMF package within Bioconductor
metaHeatmap Class and Utility Methods for NMF objects
metaHeatmap,matrix-method Class and Utility Methods for NMF objects
metaHeatmap,NMF-method Class and Utility Methods for NMF objects
metaHeatmap,NMFSet-method Class to store results from multiple runs of NMF algorithms
metaHeatmap-methods Class and Utility Methods for NMF objects
metaprofiles Layer to use the NMF package within Bioconductor
metaprofiles,NMF-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<-,NMF,matrix-method Layer to use the NMF package within Bioconductor

-- N --

name,NMFSeed-method Undocumented or Internal methods and functions for package NMF
name,NMFStrategy-method Undocumented or Internal methods and functions for package NMF
name<-,NMFSeed,character-method Undocumented or Internal methods and functions for package NMF
name<-,NMFStrategy,character-method Undocumented or Internal methods and functions for package NMF
nbasis Interface class for Nonnegative Matrix Factorisation models
nbasis,NMF-method Interface class for Nonnegative Matrix Factorisation models
newNMF Implement of the standard NMF model
newNMF,missing,ANY-method Implement of the standard NMF model
newNMF,numeric,matrix-method Implement of the standard NMF model
newNMF,numeric,missing-method Implement of the standard NMF model
newNMF,numeric,numeric-method Implement of the standard NMF model
newNMF-methods Implement of the standard NMF model
nmeta Layer to use the NMF package within Bioconductor
nmeta,NMF-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,ANY,ANY,list-method Main Interface to run NMF algorithms
nmf,ANY,ANY,missing-method Main Interface to run NMF algorithms
nmf,data.frame,ANY,ANY-method Main Interface to run NMF algorithms
nmf,ExpressionSet,ANY,ANY-method Main Interface to run NMF algorithms
nmf,matrix,numeric,character-method Main Interface to run NMF algorithms
nmf,matrix,numeric,function-method Main Interface to run NMF algorithms
nmf,matrix,numeric,NMFStrategy-method 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-deprecated Deprecated functions in NMF package
NMF-internals Undocumented or Internal methods and functions for package NMF
nmf-methods Main Interface to run NMF algorithms
NMF-utils Class and Utility Methods for NMF objects
nmf.getOption Advanced usage of package NMF
nmf.models Advanced usage of package NMF
nmf.options Advanced usage of package NMF
nmf.options.reset Advanced usage of package NMF
nmf.options.runtime Advanced usage of package NMF
nmfAlgorithm Undocumented or Internal methods and functions for package NMF
nmfApply Class and Utility Methods for NMF objects
nmfApply,NMF-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
NMFns-class Nonsmooth Nonnegative Matrix Factorization
NMFOffset-class Nonnegative Matrix Factorization with Offset
nmfSeed Undocumented or Internal methods and functions for package NMF
NMFSet-class Class to store results from multiple runs of NMF algorithms
NMFstd-class Implement of the standard NMF model
nrun Class to store results from multiple runs of NMF algorithms
nrun,NMFSet-method Class to store results from multiple runs of NMF algorithms

-- O --

objective Base Class for to store Nonnegative Matrix Factorisation results
objective,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
objective,NMFStrategy-method Undocumented or Internal methods and functions for package NMF
objective<- Base Class for to store Nonnegative Matrix Factorisation results
objective<-,NMFfit,character-method Base Class for to store Nonnegative Matrix Factorisation results
objective<-,NMFfit,function-method Base Class for to store Nonnegative Matrix Factorisation results
objective<-,NMFStrategy,character-method Undocumented or Internal methods and functions for package NMF
objective<-,NMFStrategy,function-method Undocumented or Internal methods and functions for package NMF
offset,NMFOffset-method Nonnegative Matrix Factorization with Offset

-- P --

plot.NMF.rank Estimate optimal rank for Nonnegative Matrix Factorization (NMF) models
predict Class and Utility Methods for NMF objects
predict,matrix-method Class and Utility Methods for NMF objects
predict,NMF-method Class and Utility Methods for NMF objects
predict,NMFSet-method Class to store results from multiple runs of NMF algorithms
predict-methods Class and Utility Methods for NMF objects
predict.nmf Class and Utility Methods for NMF objects
purity Class and Utility Methods for NMF objects
purity,factor,factor-method Class and Utility Methods for NMF objects
purity,NMF,factor-method Class and Utility Methods for NMF objects
purity,NMFSet,ANY-method Class to store results from multiple runs of NMF algorithms
purity,table,missing-method Class and Utility Methods for NMF objects
purity-methods Class and Utility Methods for NMF objects

-- R --

random Interface class for Nonnegative Matrix Factorisation models
random,NMF,matrix-method Interface class for Nonnegative Matrix Factorisation models
random,NMF,missing-method Interface class for Nonnegative Matrix Factorisation models
random,NMF,numeric-method Interface class for Nonnegative Matrix Factorisation models
random,NMFns,numeric-method Nonsmooth Nonnegative Matrix Factorization
random,NMFOffset,numeric-method Nonnegative Matrix Factorization with Offset
random,NMFstd,numeric-method Implement of the standard NMF model
random-methods Interface class for Nonnegative Matrix Factorisation models
residuals Class and Utility Methods for NMF objects
residuals,NMFfit-method Class and Utility Methods for NMF objects
residuals,NMFSet-method Class to store results from multiple runs of NMF algorithms
residuals<- Base Class for to store Nonnegative Matrix Factorisation results
residuals<-,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
residuals<--methods Base Class for to store Nonnegative Matrix Factorisation results
rss Class and Utility Methods for NMF objects
rss,NMF-method Class and Utility Methods for NMF objects
rss,NMFSet-method Class to store results from multiple runs of NMF algorithms
runtime Base Class for to store Nonnegative Matrix Factorisation results
runtime,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
runtime,NMFSet-method Class to store results from multiple runs of NMF algorithms

-- S --

sampleNames Interface class for Nonnegative Matrix Factorisation models
sampleNames,NMF-method Interface class for Nonnegative Matrix Factorisation models
sampleNames,NMFSet-method Class to store results from multiple runs of NMF algorithms
sampleNames<- Interface class for Nonnegative Matrix Factorisation models
sampleNames<-,NMF,ANY-method Interface class for Nonnegative Matrix Factorisation models
sampleNames<-,NMF-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,NMFfit-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<-,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
show,NMF-method Interface class for Nonnegative Matrix Factorisation models
show,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
show,NMFns-method Nonsmooth Nonnegative Matrix Factorization
show,NMFOffset-method Nonnegative Matrix Factorization with Offset
show,NMFSeed-method Undocumented or Internal methods and functions for package NMF
show,NMFSet-method Class to store results from multiple runs of NMF algorithms
show,NMFStrategy-method Undocumented or Internal methods and functions for package NMF
show,NMFStrategyIterative-method Undocumented or Internal methods and functions for package NMF
smoothing Nonsmooth Nonnegative Matrix Factorization
smoothing,NMFns-method Nonsmooth Nonnegative Matrix Factorization
smoothing-methods Nonsmooth Nonnegative Matrix Factorization
sparseness Class and Utility Methods for NMF objects
sparseness,matrix-method Class and Utility Methods for NMF objects
sparseness,NMF-method Class and Utility Methods for NMF objects
sparseness,numeric-method Class and Utility Methods for NMF objects
sparseness-methods Class and Utility Methods for NMF objects
summary,NMF-method Interface class for Nonnegative Matrix Factorisation models
summary,NMFfit-method Base Class for to store Nonnegative Matrix Factorisation results
summary,NMFSet-method Class to store results from multiple runs of NMF algorithms
syntheticNMF Class and Utility Methods for NMF objects

-- misc --

[,NMF-method Interface class for Nonnegative Matrix Factorisation models