Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
Specific NMF Layer for Bioconductor
Show method for objects of class NMFfitX1
Show method for objects of class NMFfitXn
Show method for objects of class NMFList
Show method for objects of class NMFns
Show method for objects of class NMFOffset
Show method for objects of class NMFSeed
Show method for objects of class NMFStrategyIterative
Silhouette of NMF Clustering
Smoothing Matrix in Nonsmooth NMF Models
NMF Algorithm - Sparse NMF via Alternating NNLS
Sparseness
Get/Set a Static Variable in NMF Algorithms
Comparing Results from Different NMF Runs
Defunct Functions and Classes in the NMF Package
Deprecated Functions in the Package NMF
Base Class for to store Nonnegative Matrix Factorisation results
Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
Advanced Usage of the Package NMF
Utility function to aggregate numerical quality measures from `NMFfitX...
Annotated Heatmaps
Returns the method names used to compute the NMF fits in the list. It ...
Generic Interface for Algorithms
Assessing and Comparing NMF Models
Annotation Tracks
Accessing NMF Factors
Correlations in NMF Models
Concatenating NMF Models
Testing Compatibility of Algorithm and Models
Generate Break Intervals from Numeric Variables
Builds a Color Palette from Compact Color Specification
Builds a Color Ramp from Compact Color Specification
Extract Colour Palette Specification
Error Checks in NMF Runs
Cluster Matrix Rows in Annotated Heatmaps
Clustering Connectivity and Consensus Matrices
Returns the consensus matrix computed while performing all NMF runs, a...
Computes the consensus matrix of the set of fits stored in object, a...
Hierarchical Clustering of a Consensus Matrix
Cophenetic Correlation Coefficient
Fade Out the Upper Branches from a Dendrogram
Distances and Objective Functions
Dimension names for NMF objects
Dimension of NMF Objects
Dispersion of a Matrix
Internal Routine for Fast Combinatorial Nonnegative Least-Squares
Fast Combinatorial Nonnegative Least-Square
Extracting Fitted Models
Fitted Matrix in NMF Models
NMF Multiplicative Update for NMF with Offset Models
Utilities and Extensions for Foreach Loops
NMF Algorithm/Updates for Frobenius Norm
Open a File Graphic Device
Internal Grid Extension
Heatmaps of NMF Factors
Updating Objects In Place
Package Check Utils
NMF Algorithm/Updates for Kullback-Leibler Divergence
LaTeX Utilities for Vignettes
Multiplicative Updates for LS-NMF
Internal verbosity option
Extending Annotation Vectors
NMF Multiplicative Updates for Euclidean Distance
NMF Multiplicative Updates for Kullback-Leibler Divergence
Generic Interface for Nonnegative Matrix Factorisation Models
Algorithms and framework for Nonnegative Matrix Factorization (NMF).
Testing Equality of NMF Models
Running NMF algorithms
Listing and Retrieving NMF Algorithms
Apply Function for NMF Objects
Checking NMF Algorithm
Estimate Rank for NMF Models
Factory Method for Multiple NMF Run Objects
Structure for Storing the Best Fit Amongst Multiple NMF Runs
Structure for Storing All Fits from Multiple NMF Runs
Showing Arguments of NMF Algorithms
Class for Storing Heterogeneous NMF fits
Factory Methods NMF Models
NMF Model - Nonsmooth Nonnegative Matrix Factorization
Updating NMF Objects
NMF Model - Nonnegative Matrix Factorization with Offset
Run NMF Methods and Generate a Report
Base class that defines the interface for NMF seeding methods.
Seeding Strategies for NMF Algorithms
NMF Model - Standard model
Virtual Interface for NMF Algorithms
Factory Method for NMFStrategy Objects
NMF Package Specific Options
Interface for Single Function NMF Strategies
Interface for Algorithms: Implementation for Iterative NMF Algorithms
Wrapping NMF Algorithms
Transforming from Mixed-sign to Nonnegative Data
NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorizati...
Returns the objective function associated with the algorithm that comp...
Returns the offset from the fitted model.
Offsets in NMF Models with Offset
Utilities for Parallel Computations
Simple Parsing of Formula
Plots the residual track computed at regular interval during the fit o...
Clustering and Prediction
Plotting Expression Profiles
Purity and Entropy of a Clustering
Randomizing Data
Registry for NMF Algorithms
Residuals in NMF Models
Flags a Color Palette Specification for Reversion
Generating Random Matrices
Extracting RNG Data from NMF Objects
Generating Random NMF Models
Residual Sum of Squares and Explained Variance
Returns the CPU time required to compute all NMF fits in the list. It ...
Returns the CPU time used to perform all the NMF fits stored in `objec...
Show method for objects of class NMFfit
Show method for objects of class NMFfitX
Rescaling NMF Models
Feature Selection in NMF Models
Interface for NMF Seeding Methods
Registering NMF Algorithms
NMFSeed is a constructor method that instantiate NMFSeed objects.
Computational Setup Functions
Show method for objects of class NMF
Stopping Criteria for NMF Iterative Strategies
Generic Strategy Class
Sub-setting NMF Objects
Simulating Datasets
Transformation NMF Model Objects
Fixed Terms in NMF Models
Fixed Terms in NMF Models
Simple Progress Bar
Testing NMF Objects
Utility Function in the NMF Package
Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.