NMF-package	NMF-package
$	NMFfit-class
$,NMF-method	NMF-internals
$,NMFfit-method	NMFfit-class
$<-	NMFfit-class
$<-,NMF-method	NMF-internals
$<-,NMFfit-method	NMFfit-class
algorithm	NMFfit-class
algorithm,NMFfit-method	NMFfit-class
algorithm,NMFfitXn-method	NMFfitXn
algorithm,NMFList-method	NMFList
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
as.NMFList	nmf-compare
as.NMFList,ANY-method	nmf-compare
as.NMFList-methods	nmf-compare
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
basisnames	dimnames-methods
basisnames,NMF-method	dimnames-methods
basisnames<-	dimnames-methods
basisnames<-,NMF-method	dimnames-methods
basisnames<-.NMF	dimnames-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	nmf-compare
compare,list-method	nmf-compare
compare-methods	nmf-compare
connectivity	NMF-utils
connectivity,NMF-method	NMF-utils
connectivity-methods	NMF-utils
consensus	nmf-multiple
consensus,NMF-method	NMF-class
consensus,NMFfitX-method	NMFfitX
consensus,NMFfitX1-method	NMFfitX1
consensus,NMFfitXn-method	NMFfitXn
consensus-methods	nmf-multiple
cophcor	nmf-multiple
cophcor,matrix-method	nmf-multiple
cophcor,NMFfitX-method	nmf-multiple
cophcor-methods	nmf-multiple
dim,NMF-method	NMF-class
dim,NMFfitXn-method	NMFfitXn
dimnames,NMF-method	dimnames-methods
dimnames-NMF	dimnames-methods
dimnames<-,NMF-method	dimnames-methods
dimnames<-.NMF	dimnames-methods
dispersion	nmf-multiple
dispersion,matrix-method	nmf-multiple
dispersion,NMFfitX-method	nmf-multiple
dispersion-methods	nmf-multiple
distance	NMF-class
distance,ExpressionSet,NMF-method	Bioc-layer
distance,matrix,NMF-method	NMF-class
distance,matrix,NMFfit-method	NMFfit-class
distance,missing,missing-method	NMF-class
entropy	NMF-utils
entropy,factor,factor-method	NMF-utils
entropy,NMF,ANY-method	NMF-utils
entropy,NMF,factor-method	NMF-utils
entropy,NMFfitXn,ANY-method	NMFfitXn
entropy,table,missing-method	NMF-utils
entropy-methods	NMF-utils
errorPlot	NMF-deprecated
errorPlot,ANY-method	NMF-deprecated
errorPlot,NMFfit-method	NMF-deprecated
esGolub	esGolub
evar	NMF-utils
evar,NMF-method	NMF-utils
evar-methods	NMF-utils
extra	NMF-defunct
extra,NMFfit-method	NMF-defunct
extra-methods	NMF-defunct
extractFeatures	NMF-utils
extractFeatures,NMF-method	NMF-utils
fcnnls	fcnnls
fcnnls,ANY,numeric-method	fcnnls
fcnnls,matrix,matrix-method	fcnnls
fcnnls,numeric,matrix-method	fcnnls
featureNames	NMF-class
featureNames,NMF-method	NMF-class
featureNames,NMFfitX-method	NMFfitX
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,NMFfitX-method	nmf-multiple
fit,NMFfitX1-method	NMFfitX1
fit,NMFfitXn-method	NMFfitXn
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
isNMFfit	advanced
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,NMFfitX-method	nmf-multiple
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
modelname	NMF-class
modelname,NMF-method	NMF-class
modelname,NMFfit-method	NMFfit-class
modelname,NMFStrategy-method	NMF-internals
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	NMF-deprecated
niter	NMFfit-class
niter,NMFfit-method	NMFfit-class
niter-methods	NMFfit-class
niter<-,NMFfit,numeric-method	NMFfit-class
nmeta	Bioc-layer
nmeta,NMF-method	Bioc-layer
nmeta-methods	Bioc-layer
NMF	NMF-package
nmf	nmf-methods
NMF Algorithms	nmf-methods
nmf,data.frame,ANY,ANY-method	nmf-methods
nmf,ExpressionSet,ANY,ANY-method	nmf-methods
nmf,matrix,ANY,ANY-method	nmf-methods
nmf,matrix,numeric,character-method	nmf-methods
nmf,matrix,numeric,function-method	nmf-methods
nmf,matrix,numeric,list-method	nmf-methods
nmf,matrix,numeric,NMFStrategy-method	nmf-methods
NMF-advanced	advanced
NMF-bioc	Bioc-layer
NMF-class	NMF-class
nmf-compare	nmf-compare
NMF-defunct	NMF-defunct
NMF-deprecated	NMF-deprecated
NMF-internals	NMF-internals
nmf-methods	nmf-methods
nmf-multiple	nmf-multiple
NMF-options	options
NMF-utils	NMF-utils
nmf.getOption	options
nmf.options	options
nmf.options.reset	options
nmf.options.runtime	options
nmfAlgorithm	NMF-internals
nmfApply	NMF-utils
nmfApply,NMF-method	NMF-utils
nmfEstimateRank	nmfEstimateRank
NMFfit-class	NMFfit-class
NMFfitX-class	NMFfitX
NMFfitX1-class	NMFfitX1
NMFfitXn-class	NMFfitXn
NMFList-class	NMFList
nmfModel	nmfModel
nmfModel,matrix,ANY-method	nmfModel
nmfModel,missing,ANY-method	nmfModel
nmfModel,missing,missing-method	nmfModel
nmfModel,NULL,ANY-method	nmfModel
nmfModel,numeric,matrix-method	nmfModel
nmfModel,numeric,missing-method	nmfModel
nmfModel,numeric,numeric-method	nmfModel
nmfModel-methods	nmfModel
NMFns-class	NMFns-class
NMFOffset-class	NMFOffset-class
nmfSeed	NMF-internals
NMFSet-class	NMFSet-class
NMFstd-class	NMFstd-class
nrun	nmf-multiple
nrun,NMFfit-method	NMFfit-class
nrun,NMFfitX-method	NMFfitX
nrun,NMFfitX1-method	NMFfitX1
nrun,NMFfitXn-method	NMFfitXn
nrun-methods	nmf-multiple
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,NMFfit,missing-method	NMF-utils
plot,NMFfit-method	NMF-utils
plot,NMFList,missing-method	nmf-compare
plot,NMFList-method	nmf-compare
plot.NMF.rank	nmfEstimateRank
predict	NMF-utils
predict,matrix-method	NMF-utils
predict,NMF-method	NMF-utils
predict,NMFfitXn-method	nmf-multiple
predict-methods	NMF-utils
purity	NMF-utils
purity,factor,factor-method	NMF-utils
purity,NMF,ANY-method	NMF-utils
purity,NMF,factor-method	NMF-utils
purity,NMFfitXn,ANY-method	NMFfitXn
purity,table,missing-method	NMF-utils
purity-methods	NMF-utils
randomize	NMF-utils
residuals	NMF-utils
residuals,NMFfit-method	NMF-utils
residuals,NMFfitXn-method	NMFfitXn
residuals<-	NMFfit-class
residuals<-,NMFfit-method	NMFfit-class
residuals<--methods	NMFfit-class
rmatrix	rmatrix
rnmf	NMF-class
rnmf,NMF,matrix-method	NMF-class
rnmf,NMF,missing-method	NMF-class
rnmf,NMF,numeric-method	NMF-class
rnmf,NMFOffset,numeric-method	NMFOffset-class
rnmf-methods	NMF-class
rss	NMF-utils
rss,NMF-method	NMF-utils
runtime	NMFfit-class
runtime,NMFfit-method	NMFfit-class
runtime,NMFList-method	NMFList
runtime.all	nmf-multiple
runtime.all,NMFfit-method	NMFfit-class
runtime.all,NMFfitX-method	nmf-multiple
runtime.all,NMFfitX1-method	NMFfitX1
runtime.all,NMFfitXn-method	nmf-multiple
runtime.all-methods	nmf-multiple
sampleNames	NMF-class
sampleNames,NMF-method	NMF-class
sampleNames,NMFfitX-method	NMFfitX
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
seqtime	nmf-multiple
seqtime,NMFfitXn-method	NMFfitXn
seqtime-methods	nmf-multiple
show,NMF-method	NMF-class
show,NMFfit-method	NMFfit-class
show,NMFfitX-method	NMFfitX
show,NMFfitX1-method	NMFfitX1
show,NMFfitXn-method	NMFfitXn
show,NMFList-method	NMFList
show,NMFns-method	NMFns-class
show,NMFOffset-method	NMFOffset-class
show,NMFSeed-method	NMF-internals
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
subset-NMF	NMF[-methods
summary,NMF-method	NMF-class
summary,NMFfit-method	NMFfit-class
summary,NMFfitX-method	nmf-multiple
summary,NMFList-method	nmf-compare
syntheticNMF	NMF-utils
[,NMF-method	NMF[-methods
