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