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