NMF-package	NMF-package
algorithm	NMFfit-class
algorithm,NMFfit-method	NMFfit-class
algorithm,NMFSet-method	NMFSet-class
algorithm,NMFStrategyFunction-method	NMF-internals
algorithm<-	NMFfit-class
algorithm<-,NMFfit,ANY-method	NMFfit-class
algorithm<-,NMFStrategyFunction,character-method	NMF-internals
algorithm<-,NMFStrategyFunction,function-method	NMF-internals
basis	basis-methods
basis,NMF-method	basis-methods
basis,NMFfit-method	NMFfit-class
basis,NMFstd-method	NMFstd-class
basis-methods	basis-methods
basis<-	basis-methods
basis<-,NMF,matrix-method	basis-methods
basis<-,NMFfit,matrix-method	NMFfit-class
basis<-,NMFstd,matrix-method	NMFstd-class
basis<--methods	basis-methods
clusters	NMF-deprecated
clusters,matrix-method	NMF-deprecated
clusters,NMF-method	NMF-deprecated
clusters-methods	NMF-deprecated
coef	basis-methods
coef,NMF-method	basis-methods
coef,NMFfit-method	NMFfit-class
coef,NMFstd-method	NMFstd-class
coef<-	basis-methods
coef<-,NMF,matrix-method	basis-methods
coef<-,NMFfit,matrix-method	NMFfit-class
coef<-,NMFstd,matrix-method	NMFstd-class
coef<--methods	basis-methods
coefficients	basis-methods
coefficients,NMF-method	basis-methods
coefficients<-,NMF,matrix-method	basis-methods
compare	NMFSet-class
compare,list-method	NMFSet-class
compare,NMFSet-method	NMFSet-class
connectivity	NMF-utils
connectivity,NMF-method	NMF-utils
connectivity,NMFSet-method	NMFSet-class
connectivity-methods	NMF-utils
cophcor	NMF-utils
cophcor,matrix-method	NMF-utils
cophcor,NMFSet-method	NMFSet-class
cophcor-methods	NMF-utils
dim,NMF-method	NMF-class
dispersion	NMF-utils
dispersion,matrix-method	NMF-utils
dispersion,NMFSet-method	NMFSet-class
dispersion-methods	NMF-utils
distance	NMF-class
distance,matrix,NMF-method	NMF-class
distance,matrix,NMFfit-method	NMFfit-class
entropy	NMF-utils
entropy,factor,factor-method	NMF-utils
entropy,NMF,factor-method	NMF-utils
entropy,NMFSet,ANY-method	NMFSet-class
entropy,table,missing-method	NMF-utils
entropy-methods	NMF-utils
errorPlot	NMFfit-class
errorPlot,NMFfit-method	NMFfit-class
errorPlot,NMFSet-method	NMFSet-class
esGolub	esGolub
extra	NMFfit-class
extra,NMFfit-method	NMFfit-class
extra-methods	NMFfit-class
extractFeatures	NMF-utils
extractFeatures,NMF-method	NMF-utils
featureNames	NMF-class
featureNames,NMF-method	NMF-class
featureNames,NMFSet-method	NMFSet-class
featureNames<-	NMF-class
featureNames<-,NMF-method	NMF-class
featureScore	NMF-utils
featureScore,matrix-method	NMF-utils
featureScore,NMF-method	NMF-utils
fit	NMFfit-class
fit,NMFfit-method	NMFfit-class
fit,NMFSet-method	NMFSet-class
fit-methods	NMFfit-class
fit<-	NMFfit-class
fit<-,NMFfit,NMF-method	NMFfit-class
fitted,NMF-method	NMF-class
fitted,NMFfit-method	NMFfit-class
fitted,NMFns-method	NMFns-class
fitted,NMFOffset-method	NMFOffset-class
fitted,NMFstd-method	NMFstd-class
initialize,NMFOffset-method	NMFOffset-class
is.empty.nmf	NMF-class
is.empty.nmf,NMF-method	NMF-class
join	NMFSet-class
join,list-method	NMFSet-class
metagenes	Bioc-layer
metagenes,NMF-method	Bioc-layer
metagenes-methods	Bioc-layer
metagenes<-	Bioc-layer
metagenes<-,NMF,matrix-method	Bioc-layer
metaHeatmap	NMF-utils
metaHeatmap,matrix-method	NMF-utils
metaHeatmap,NMF-method	NMF-utils
metaHeatmap,NMFSet-method	NMFSet-class
metaHeatmap-methods	NMF-utils
metaprofiles	Bioc-layer
metaprofiles,NMF-method	Bioc-layer
metaprofiles-methods	Bioc-layer
metaprofiles<-	Bioc-layer
metaprofiles<-,NMF,matrix-method	Bioc-layer
name,NMFSeed-method	NMF-internals
name,NMFStrategy-method	NMF-internals
name<-,NMFSeed,character-method	NMF-internals
name<-,NMFStrategy,character-method	NMF-internals
nbasis	NMF-class
nbasis,NMF-method	NMF-class
newNMF	NMFstd-class
newNMF,missing,ANY-method	NMFstd-class
newNMF,numeric,matrix-method	NMFstd-class
newNMF,numeric,missing-method	NMFstd-class
newNMF,numeric,numeric-method	NMFstd-class
newNMF-methods	NMFstd-class
nmeta	Bioc-layer
nmeta,NMF-method	Bioc-layer
nmeta-methods	Bioc-layer
NMF	NMF-package
nmf	nmf-methods
NMF Algorithms	nmf-methods
nmf,ANY,ANY,list-method	nmf-methods
nmf,ANY,ANY,missing-method	nmf-methods
nmf,data.frame,ANY,ANY-method	nmf-methods
nmf,ExpressionSet,ANY,ANY-method	nmf-methods
nmf,matrix,numeric,character-method	nmf-methods
nmf,matrix,numeric,function-method	nmf-methods
nmf,matrix,numeric,NMFStrategy-method	nmf-methods
NMF-advanced	advanced
NMF-bioc	Bioc-layer
NMF-class	NMF-class
NMF-deprecated	NMF-deprecated
NMF-internals	NMF-internals
nmf-methods	nmf-methods
NMF-utils	NMF-utils
nmf.getOption	advanced
nmf.models	advanced
nmf.options	advanced
nmf.options.reset	advanced
nmf.options.runtime	advanced
nmfAlgorithm	NMF-internals
nmfApply	NMF-utils
nmfApply,NMF-method	NMF-utils
nmfEstimateRank	nmfEstimateRank
NMFfit-class	NMFfit-class
NMFns-class	NMFns-class
NMFOffset-class	NMFOffset-class
nmfSeed	NMF-internals
NMFSet-class	NMFSet-class
NMFstd-class	NMFstd-class
nrun	NMFSet-class
nrun,NMFSet-method	NMFSet-class
objective	NMFfit-class
objective,NMFfit-method	NMFfit-class
objective,NMFStrategy-method	NMF-internals
objective<-	NMFfit-class
objective<-,NMFfit,character-method	NMFfit-class
objective<-,NMFfit,function-method	NMFfit-class
objective<-,NMFStrategy,character-method	NMF-internals
objective<-,NMFStrategy,function-method	NMF-internals
offset,NMFOffset-method	NMFOffset-class
plot.NMF.rank	nmfEstimateRank
predict	NMF-utils
predict,matrix-method	NMF-utils
predict,NMF-method	NMF-utils
predict,NMFSet-method	NMFSet-class
predict-methods	NMF-utils
predict.nmf	NMF-utils
purity	NMF-utils
purity,factor,factor-method	NMF-utils
purity,NMF,factor-method	NMF-utils
purity,NMFSet,ANY-method	NMFSet-class
purity,table,missing-method	NMF-utils
purity-methods	NMF-utils
random	NMF-class
random,NMF,matrix-method	NMF-class
random,NMF,missing-method	NMF-class
random,NMF,numeric-method	NMF-class
random,NMFns,numeric-method	NMFns-class
random,NMFOffset,numeric-method	NMFOffset-class
random,NMFstd,numeric-method	NMFstd-class
random-methods	NMF-class
residuals	NMF-utils
residuals,NMFfit-method	NMF-utils
residuals,NMFSet-method	NMFSet-class
residuals<-	NMFfit-class
residuals<-,NMFfit-method	NMFfit-class
residuals<--methods	NMFfit-class
rss	NMF-utils
rss,NMF-method	NMF-utils
rss,NMFSet-method	NMFSet-class
runtime	NMFfit-class
runtime,NMFfit-method	NMFfit-class
runtime,NMFSet-method	NMFSet-class
sampleNames	NMF-class
sampleNames,NMF-method	NMF-class
sampleNames,NMFSet-method	NMFSet-class
sampleNames<-	NMF-class
sampleNames<-,NMF,ANY-method	NMF-class
sampleNames<-,NMF-method	NMF-class
seed	nmf-methods
seeding	NMFfit-class
seeding,NMFfit-method	NMFfit-class
seeding-methods	NMFfit-class
seeding<-	NMFfit-class
seeding<-,NMFfit-method	NMFfit-class
show,NMF-method	NMF-class
show,NMFfit-method	NMFfit-class
show,NMFns-method	NMFns-class
show,NMFOffset-method	NMFOffset-class
show,NMFSeed-method	NMF-internals
show,NMFSet-method	NMFSet-class
show,NMFStrategy-method	NMF-internals
show,NMFStrategyIterative-method	NMF-internals
smoothing	NMFns-class
smoothing,NMFns-method	NMFns-class
smoothing-methods	NMFns-class
sparseness	NMF-utils
sparseness,matrix-method	NMF-utils
sparseness,NMF-method	NMF-utils
sparseness,numeric-method	NMF-utils
sparseness-methods	NMF-utils
summary,NMF-method	NMF-class
summary,NMFfit-method	NMFfit-class
summary,NMFSet-method	NMFSet-class
syntheticNMF	NMF-utils
[,NMF-method	NMF-class
