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