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 |
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,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 |
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 |
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 |
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 |
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 |
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 |
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 |