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