| 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 |