.fcnnls                 Internal Routine for Fast Combinatorial
                        Nonnegative Least-Squares
NMF-class               Generic Interface for Nonnegative Matrix
                        Factorisation Models
NMF-defunct             Defunct Functions and Classes in the NMF
                        Package
NMF-deprecated          Deprecated Functions in the Package NMF
NMF-package             Algorithms and framework for Nonnegative Matrix
                        Factorization (NMF).
NMFList-class           Class for Storing Heterogeneous NMF fits
NMFOffset-class         NMF Model - Nonnegative Matrix Factorization
                        with Offset
NMFSeed                 'NMFSeed' is a constructor method that
                        instantiate 'NMFSeed' objects.
NMFSeed-class           Base class that defines the interface for NMF
                        seeding methods.
NMFStop                 Stopping Criteria for NMF Iterative Strategies
NMFStrategy             Factory Method for NMFStrategy Objects
NMFStrategyFunction-class
                        Interface for Single Function NMF Strategies
NMFStrategyIterative-class
                        Interface for Algorithms: Implementation for
                        Iterative NMF Algorithms
NMFStrategyOctave-class
                        S4 Interface for Octave-Matlab NMF Algorithms
NMFfit-class            Base Class for to store Nonnegative Matrix
                        Factorisation results
NMFfitX-class           Virtual Class to Handle Results from Multiple
                        Runs of NMF Algorithms
NMFfitX1-class          Structure for Storing the Best Fit Amongst
                        Multiple NMF Runs
NMFfitXn-class          Structure for Storing All Fits from Multiple
                        NMF Runs
NMFns-class             NMF Model - Nonsmooth Nonnegative Matrix
                        Factorization
NMFstd-class            NMF Model - Standard model
[,NMF-method            Sub-setting NMF Objects
advanced-NMF            Advanced Usage of the Package NMF
aheatmap                Annotated Heatmaps
algorithm,NMFList-method
                        Returns the method names used to compute the
                        NMF fits in the list. It returns 'NULL' if the
                        list is empty.
algorithm,NMFStrategyOctave-method
                        Returns the name of the Octave/Matlab function
                        that implements the NMF algorithm - as stored
                        in slot 'algorithm'.
algorithmic-NMF         Generic Interface for Algorithms
basis                   Accessing NMF Factors
basiscor                Correlations in NMF Models
basisnames              Dimension names for NMF objects
bioc-NMF                Specific NMF Layer for Bioconductor
canFit                  Testing Compatibility of Algorithm and Models
compare-NMF             Comparing Results from Different NMF Runs
connectivity            Clustering Connectivity and Consensus Matrices
consensus,NMFfitX1-method
                        Returns the consensus matrix computed while
                        performing all NMF runs, amongst which 'object'
                        was selected as the best fit.
consensus,NMFfitXn-method
                        Computes the consensus matrix of the set of
                        fits stored in 'object', as the mean
                        connectivity matrix across runs.
consensushc             Hierarchical Clustering of a Consensus Matrix
cophcor                 Cophenetic Correlation Coefficient
deviance                Distances and Objective Functions
dispersion              Dispersion of a Matrix
esGolub                 Golub ExpressionSet
fcnnls                  Fast Combinatorial Nonnegative Least-Square
featureScore            Feature Selection in NMF Models
fit                     Extracting Fitted Models
fitted                  Fitted Matrix in NMF Models
getRNG1                 Extracting RNG Data from NMF Objects
heatmap-NMF             Heatmaps of NMF Factors
ibterms                 Fixed Terms in NMF Models
is.nmf                  Testing NMF Objects
match_atrack            Extending Annotation Vectors
methods-NMF             Registry for NMF Algorithms
nbasis                  Dimension of NMF Objects
nmf                     Running NMF algorithms
nmf.equal               Testing Equality of NMF Models
nmfAlgorithm            Listing and Retrieving NMF Algorithms
nmfAlgorithm.SNMF_R     NMF Algorithm - Sparse NMF via Alternating NNLS
nmfApply                Apply Function for NMF Objects
nmfCheck                Checking NMF Algorithm
nmfEstimateRank         Estimate Rank for NMF Models
nmfFormals              Showing Arguments of NMF Algorithms
nmfModel                Factory Methods NMF Models
nmfObject               Updating NMF Objects
nmfReport               Run NMF Methods and Generate a Report
nmfSeed                 Seeding Strategies for NMF Algorithms
nmf_update.KL.h         NMF Multiplicative Updates for Kullback-Leibler
                        Divergence
nmf_update.brunet_R     NMF Algorithm/Updates for Kullback-Leibler
                        Divergence
nmf_update.euclidean.h
                        NMF Multiplicative Updates for Euclidean
                        Distance
nmf_update.euclidean_offset.h
                        NMF Multiplicative Update for NMF with Offset
                        Models
nmf_update.lee_R        NMF Algorithm/Updates for Frobenius Norm
nmf_update.lsnmf        Multiplicative Updates for LS-NMF
nmf_update.ns           NMF Multiplicative Update for Nonsmooth
                        Nonnegative Matrix Factorization (nsNMF).
nneg                    Transforming from Mixed-sign to Nonnegative
                        Data
objective,NMFfit-method
                        Returns the objective function associated with
                        the algorithm that computed the fitted NMF
                        model 'object', or the objective value with
                        respect to a given target matrix 'y' if it is
                        supplied.
offset,NMFOffset-method
                        Offsets in NMF Models with Offset
offset,NMFfit-method    Returns the offset from the fitted model.
options-NMF             NMF Package Specific Options
parallel-NMF            Utilities for Parallel Computations
plot,NMFfit,missing-method
                        Plots the residual track computed at regular
                        interval during the fit of the NMF model 'x'.
predict                 Clustering and Prediction
profplot                Plotting Expression Profiles
purity                  Purity and Entropy of a Clustering
randomize               Randomizing Data
residuals               Residuals in NMF Models
rmatrix                 Generating Random Matrices
rnmf                    Generating Random NMF Models
rss                     Residual Sum of Squares and Explained Variance
runtime,NMFList-method
                        Returns the CPU time required to compute all
                        NMF fits in the list. It returns 'NULL' if the
                        list is empty. If no timing data are available,
                        the sequential time is returned.
runtime.all,NMFfitXn-method
                        Returns the CPU time used to perform all the
                        NMF fits stored in 'object'.
scale.NMF               Rescaling NMF Models
seed                    Interface for NMF Seeding Methods
setNMFMethod            Registering NMF Algorithms
setupBackend            Computational Setup Functions
show,NMF-method         Show method for objects of class 'NMF'
show,NMFList-method     Show method for objects of class 'NMFList'
show,NMFOffset-method   Show method for objects of class 'NMFOffset'
show,NMFSeed-method     Show method for objects of class 'NMFSeed'
show,NMFStrategyIterative-method
                        Show method for objects of class
                        'NMFStrategyIterative'
show,NMFfit-method      Show method for objects of class 'NMFfit'
show,NMFfitX-method     Show method for objects of class 'NMFfitX'
show,NMFfitX1-method    Show method for objects of class 'NMFfitX1'
show,NMFfitXn-method    Show method for objects of class 'NMFfitXn'
show,NMFns-method       Show method for objects of class 'NMFns'
silhouette.NMF          Silhouette of NMF Clustering
smoothing               Smoothing Matrix in Nonsmooth NMF Models
sparseness              Sparseness
staticVar               Get/Set a Static Variable in NMF Algorithms
summary                 Assessing and Comparing NMF Models
syntheticNMF            Simulating Datasets
t.NMF                   Transformation NMF Model Objects
utils-NMF               Utility Function in the NMF Package
