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