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