NMF Algorithm/Updates for Kullback-Leibler Divergence
Virtual Interface for NMF Algorithms
Advanced Usage of the Package NMF
Structure for Storing All Fits from Multiple NMF Runs
Generic Strategy Class
Builds a Color Ramp from Compact Color Specification
Dimension names for NMF objects
Utilities and Extensions for Foreach Loops
Fitted Matrix in NMF Models
Apply Function for NMF Objects
Generating Random Matrices
Flags a Color Palette Specification for Reversion
Show method for objects of class NMF
Get/Set a Static Variable in NMF Algorithms
Show method for objects of class NMFfitX
Utility Function in the NMF Package
Generate Break Intervals from Numeric Variables
Specific NMF Layer for Bioconductor
Concatenating NMF Models
Internal Routine for Fast Combinatorial Nonnegative Least-Squares
Fade Out the Upper Branches from a Dendrogram
nmf_update.euclidean_offset.h
NMF Multiplicative Update for NMF with Offset Models
Utilities for Parallel Computations
Clustering and Prediction
Base Class for to store Nonnegative Matrix Factorisation results
Annotated Heatmaps
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.
Extract Colour Palette Specification
Registry for NMF Algorithms
Generic Interface for Nonnegative Matrix Factorisation Models
NMFStrategyFunction-class
Interface for Single Function NMF Strategies
Error Checks in NMF Runs
Defunct Functions and Classes in the NMF Package
Builds a Color Palette from Compact Color Specification
Correlations in NMF Models
Comparing Results from Different NMF Runs
Dimension of NMF Objects
Updating Objects In Place
Updating NMF Objects
Returns the offset from the fitted model.
Checking NMF Algorithm
Interface for NMF Seeding Methods
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.
Factory Method for NMFStrategy Objects
Factory Method for Multiple NMF Run Objects
S4 Interface for Octave-Matlab NMF Algorithms
Show method for objects of class NMFOffset
Structure for Storing the Best Fit Amongst Multiple NMF Runs
Sparseness
Returns the method names used to compute the NMF fits in the list.
It returns NULL
if the list is empty.
NMF Model - Standard model
Stopping Criteria for NMF Iterative Strategies
Show method for objects of class NMFfitXn
NMF Algorithm/Updates for Frobenius Norm
Algorithms and framework for Nonnegative Matrix Factorization (NMF).
NMFStrategyIterative-class
Interface for Algorithms: Implementation for Iterative NMF Algorithms
Distances and Objective Functions
Estimate Rank for NMF Models
NMF Model - Nonnegative Matrix Factorization with Offset
Registering NMF Algorithms
Heatmaps of NMF Factors
Transforming from Mixed-sign to Nonnegative Data
Randomizing Data
algorithm,NMFStrategyOctave-method
Returns the name of the Octave/Matlab function that implements the NMF algorithm -- as stored in
slot algorithm
.
Dispersion of a Matrix
Accessing NMF Factors
Show method for objects of class NMFList
Annotation Tracks
Show method for objects of class NMFfitX1
NMF Model - Nonsmooth Nonnegative Matrix Factorization
show,NMFStrategyIterative-method
Show method for objects of class NMFStrategyIterative
Clustering Connectivity and Consensus Matrices
Hierarchical Clustering of a Consensus Matrix
Extending Annotation Vectors
Factory Methods NMF Models
NMF Multiplicative Updates for Kullback-Leibler Divergence
Fast Combinatorial Nonnegative Least-Square
Seeding Strategies for NMF Algorithms
Residual Sum of Squares and Explained Variance
Plotting Expression Profiles
Residuals in NMF Models
Showing Arguments of NMF Algorithms
Computational Setup Functions
Class for Storing Heterogeneous NMF fits
NMF Algorithm - Sparse NMF via Alternating NNLS
Internal verbosity option
Fixed Terms in NMF Models
NMF Multiplicative Updates for Euclidean Distance
Simple Progress Bar
Simulating Datasets
Extracting Fitted Models
Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
Testing NMF Objects
Running NMF algorithms
Listing and Retrieving NMF Algorithms
Simple Parsing of Formula
Offsets in NMF Models with Offset
Generating Random NMF Models
Sub-setting NMF Objects
Show method for objects of class NMFSeed
Transformation NMF Model Objects
Show method for objects of class NMFns
Rescaling NMF Models
Show method for objects of class NMFfit
Generic Interface for Algorithms
Cluster Matrix Rows in Annotated Heatmaps
Cophenetic Correlation Coefficient
Deprecated Functions in the Package NMF
Multiplicative Updates for LS-NMF
Grid Internal Functions
Testing Equality of NMF Models
plot,NMFfit,missing-method
Plots the residual track computed at regular interval during the fit of
the NMF model x
.
NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
Purity and Entropy of a Clustering
Testing Compatibility of Algorithm and Models
Wrapping NMF Algorithms
Extracting RNG Data from NMF Objects
Base class that defines the interface for NMF seeding methods.
Assessing and Comparing NMF Models
Open a File Graphic Device
consensus,NMFfitX1-method
Returns the consensus matrix computed while performing all NMF runs,
amongst which object
was selected as the best fit.
Golub ExpressionSet
consensus,NMFfitXn-method
Computes the consensus matrix of the set of fits stored in object
, as
the mean connectivity matrix across runs.
NMF Package Specific Options
runtime.all,NMFfitXn-method
Returns the CPU time used to perform all the NMF fits stored in object
.
Feature Selection in NMF Models
Smoothing Matrix in Nonsmooth NMF Models
Fixed Terms in NMF Models