| basis |
Extract/Set the matrix of basis vectors from a NMF model |
| basis-method |
Base Class for to store Nonnegative Matrix Factorisation results |
| basis-method |
Implement of the standard NMF model |
| basis-method |
Extract/Set the matrix of basis vectors from a 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<--method |
Base Class for to store Nonnegative Matrix Factorisation results |
| basis<--method |
Implement of the standard NMF model |
| basis<--method |
Extract/Set the matrix of basis vectors from a NMF model |
| basis<--methods |
Extract/Set the matrix of basis vectors from a NMF model |
| coef |
Extract/Set the matrix of basis vectors from a NMF model |
| coef-method |
Base Class for to store Nonnegative Matrix Factorisation results |
| coef-method |
Implement of the standard NMF model |
| coef-method |
Extract/Set the matrix of basis vectors from a NMF model |
| coef<- |
Extract/Set the matrix of basis vectors from a NMF model |
| coef<--method |
Base Class for to store Nonnegative Matrix Factorisation results |
| coef<--method |
Implement of the standard NMF model |
| coef<--method |
Extract/Set the matrix of basis vectors from a 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-method |
Extract/Set the matrix of basis vectors from a NMF model |
| coefficients<--method |
Extract/Set the matrix of basis vectors from 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 |
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 |
| 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 |
Interface Class for Nonnegative Matrix Factorisation Models |
| dimnames<--method |
Interface Class for Nonnegative Matrix Factorisation Models |
| 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 |
| 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 |
| nbasis |
Interface Class for Nonnegative Matrix Factorisation Models |
| nbasis-method |
Interface Class for Nonnegative Matrix Factorisation Models |
| 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-utils |
Class and Utility Methods for NMF objects |
| nmf.getOption |
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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |