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 |
Comparing Results from Different NMF Runs |
compare,list-method |
Comparing Results from Different NMF Runs |
compare-methods |
Comparing Results from Different NMF Runs |
connectivity |
Class and Utility Methods for NMF objects |
connectivity,NMF-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,NMF-method |
Interface Class for Nonnegative Matrix Factorisation Models |
consensus,NMFfitX-method |
Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms |
consensus,NMFfitX1-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept |
consensus,NMFfitXn-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,matrix-method |
Handling Results from Multiple NMF Runs |
cophcor,NMFfitX-method |
Handling Results from Multiple NMF Runs |
cophcor-methods |
Handling Results from Multiple NMF Runs |
dim,NMF-method |
Interface Class for Nonnegative Matrix Factorisation Models |
dim,NMFfitXn-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits |
dimnames,NMF-method |
Interface Class for Nonnegative Matrix Factorisation Models |
dimnames<-,NMF-method |
Interface Class for Nonnegative Matrix Factorisation Models |
dispersion |
Handling Results from Multiple NMF Runs |
dispersion,matrix-method |
Handling Results from Multiple NMF Runs |
dispersion,NMFfitX-method |
Handling Results from Multiple NMF Runs |
dispersion-methods |
Handling Results from Multiple NMF Runs |
distance |
Interface Class for Nonnegative Matrix Factorisation Models |
distance,ExpressionSet,NMF-method |
Layer to use the NMF package within Bioconductor |
distance,matrix,NMF-method |
Interface Class for Nonnegative Matrix Factorisation Models |
distance,matrix,NMFfit-method |
Base Class for to store Nonnegative Matrix Factorisation results |
distance,missing,missing-method |
Interface Class for Nonnegative Matrix Factorisation Models |
entropy |
Class and Utility Methods for NMF objects |
entropy,factor,factor-method |
Class and Utility Methods for NMF objects |
entropy,NMF,ANY-method |
Class and Utility Methods for NMF objects |
entropy,NMF,factor-method |
Class and Utility Methods for NMF objects |
entropy,NMFfitXn,ANY-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits |
entropy,table,missing-method |
Class and Utility Methods for NMF objects |
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,NMF-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,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,NMFfitX-method |
Virtual Class to Handle Results from Multiple Runs of a 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,NMFfitX-method |
Handling Results from Multiple NMF Runs |
fit,NMFfitX1-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept |
fit,NMFfitXn-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits |
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 |
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,NMFfitX-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,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 |
modelname |
Interface Class for Nonnegative Matrix Factorisation Models |
modelname,NMF-method |
Interface Class for Nonnegative Matrix Factorisation Models |
modelname,NMFfit-method |
Base Class for to store Nonnegative Matrix Factorisation results |
nbasis |
Interface Class for Nonnegative Matrix Factorisation Models |
nbasis,NMF-method |
Interface Class for Nonnegative Matrix Factorisation Models |
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,data.frame,ANY,ANY-method |
Main Interface to run NMF algorithms |
nmf,ExpressionSet,ANY,ANY-method |
Main Interface to run NMF algorithms |
nmf,matrix,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,list-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-compare |
Comparing Results from Different NMF Runs |
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,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 |
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,matrix,ANY-method |
Factory Method for NMF Models |
nmfModel,missing,ANY-method |
Factory Method for NMF Models |
nmfModel,missing,missing-method |
Factory Method for NMF Models |
nmfModel,NULL,ANY-method |
Factory Method for NMF Models |
nmfModel,numeric,matrix-method |
Factory Method for NMF Models |
nmfModel,numeric,missing-method |
Factory Method for NMF Models |
nmfModel,numeric,numeric-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,NMFfit-method |
Base Class for to store Nonnegative Matrix Factorisation results |
nrun,NMFfitX-method |
Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms |
nrun,NMFfitX1-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept |
nrun,NMFfitXn-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,NMFfit,missing-method |
Class and Utility Methods for NMF objects |
plot,NMFfit-method |
Class and Utility Methods for NMF objects |
plot,NMFList,missing-method |
Comparing Results from Different NMF Runs |
plot,NMFList-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,matrix-method |
Class and Utility Methods for NMF objects |
predict,NMF-method |
Class and Utility Methods for NMF objects |
predict,NMFfitXn-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,factor,factor-method |
Class and Utility Methods for NMF objects |
purity,NMF,ANY-method |
Class and Utility Methods for NMF objects |
purity,NMF,factor-method |
Class and Utility Methods for NMF objects |
purity,NMFfitXn,ANY-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits |
purity,table,missing-method |
Class and Utility Methods for NMF objects |
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,NMFfit-method |
Class and Utility Methods for NMF objects |
residuals,NMFfitXn-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<-,NMFfit-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,NMF,matrix-method |
Interface Class for Nonnegative Matrix Factorisation Models |
rnmf,NMF,missing-method |
Interface Class for Nonnegative Matrix Factorisation Models |
rnmf,NMF,numeric-method |
Interface Class for Nonnegative Matrix Factorisation Models |
rnmf,NMFOffset,numeric-method |
Nonnegative Matrix Factorization with Offset |
rnmf-methods |
Interface Class for Nonnegative Matrix Factorisation Models |
rss |
Class and Utility Methods for NMF objects |
rss,NMF-method |
Class and Utility Methods for NMF objects |
runtime |
Base Class for to store Nonnegative Matrix Factorisation results |
runtime,NMFfit-method |
Base Class for to store Nonnegative Matrix Factorisation results |
runtime,NMFList-method |
Class "NMFList" to Handle the Comparison of NMF Results |
runtime.all |
Handling Results from Multiple NMF Runs |
runtime.all,NMFfit-method |
Base Class for to store Nonnegative Matrix Factorisation results |
runtime.all,NMFfitX-method |
Handling Results from Multiple NMF Runs |
runtime.all,NMFfitX1-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept |
runtime.all,NMFfitXn-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,NMF-method |
Interface Class for Nonnegative Matrix Factorisation Models |
sampleNames,NMFfitX-method |
Virtual Class to Handle Results from Multiple Runs of a 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 |
seqtime |
Handling Results from Multiple NMF Runs |
seqtime,NMFfitXn-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,NMF-method |
Interface Class for Nonnegative Matrix Factorisation Models |
show,NMFfit-method |
Base Class for to store Nonnegative Matrix Factorisation results |
show,NMFfitX-method |
Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms |
show,NMFfitX1-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept |
show,NMFfitXn-method |
Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits |
show,NMFList-method |
Class "NMFList" to Handle the Comparison of NMF Results |
show,NMFns-method |
Nonsmooth Nonnegative Matrix Factorization |
show,NMFOffset-method |
Nonnegative Matrix Factorization with Offset |
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,NMFfitX-method |
Handling Results from Multiple NMF Runs |
summary,NMFList-method |
Comparing Results from Different NMF Runs |
syntheticNMF |
Class and Utility Methods for NMF objects |