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NMF

Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

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.

Functions (129)

Frobenius-nmf

NMF Algorithm/Updates for Frobenius Norm

KL-nmf

NMF Algorithm/Updates for Kullback-Leibler Divergence

NMF-class

Generic Interface for Nonnegative Matrix Factorisation Models

NMF-defunct

Defunct Functions and Classes in the NMF Package

NMF-deprecated

Deprecated Functions in the Package NMF

NMF-package

Algorithms and framework for Nonnegative Matrix Factorization (NMF).

NMFList-class

Class for Storing Heterogeneous NMF fits

NMFOffset-class

NMF Model - Nonnegative Matrix Factorization with Offset

NMFSeed-class

Base class that defines the interface for NMF seeding methods.

NMFStrategy

Factory Method for NMFStrategy Objects

NMFStrategy-class

Virtual Interface for NMF Algorithms

NMFStrategyFunction-class

Interface for Single Function NMF Strategies

NMFStrategyIterative-class

Interface for Algorithms: Implementation for Iterative NMF Algorithms

NMFfit-class

Base Class for to store Nonnegative Matrix Factorisation results

NMFfitX

Factory Method for Multiple NMF Run Objects

NMFfitX-class

Virtual Class to Handle Results from Multiple Runs of NMF Algorithms

NMFfitX1-class

Structure for Storing the Best Fit Amongst Multiple NMF Runs

NMFfitXn-class

Structure for Storing All Fits from Multiple NMF Runs

NMFns-class

NMF Model - Nonsmooth Nonnegative Matrix Factorization

NMFstd-class

NMF Model - Standard model

RNG

Extracting RNG Data from NMF Objects

SNMF-nmf

NMF Algorithm - Sparse NMF via Alternating NNLS

Strategy-class

Generic Strategy Class

advanced

Advanced Usage of the Package NMF

aheatmap

Annotated Heatmaps

algorithm-commaNMFList-method

Returns the method names used to compute the NMF fits in the list. It returns NULL if the list is empty.

algorithmic

Generic Interface for Algorithms

assess

Assessing and Comparing NMF Models

atrack

Annotation Tracks

basis-coef-methods

Accessing NMF Factors

basiscor

Correlations in NMF Models

bioc

Specific NMF Layer for Bioconductor

c-commaNMF-method

Concatenating NMF Models

canFit

Testing Compatibility of Algorithm and Models

ccBreaks

Generate Break Intervals from Numeric Variables

ccPalette

Builds a Color Palette from Compact Color Specification

ccRamp

Builds a Color Ramp from Compact Color Specification

ccSpec

Extract Colour Palette Specification

checkErrors

Error Checks in NMF Runs

cluster_mat

Cluster Matrix Rows in Annotated Heatmaps

connectivity

Clustering Connectivity and Consensus Matrices

consensus-commaNMFfitX1-method

Returns the consensus matrix computed while performing all NMF runs, amongst which object was selected as the best fit.

consensus-commaNMFfitXn-method

Computes the consensus matrix of the set of fits stored in object, as the mean connectivity matrix across runs.

consensushc

Hierarchical Clustering of a Consensus Matrix

cophcor

Cophenetic Correlation Coefficient

cutdendro

Fade Out the Upper Branches from a Dendrogram

deviance

Distances and Objective Functions

dimnames

Dimension names for NMF objects

dims

Dimension of NMF Objects

dispersion

Dispersion of a Matrix

dot-fcnnls

Internal Routine for Fast Combinatorial Nonnegative Least-Squares

esGolub

Golub ExpressionSet

fcnnls

Fast Combinatorial Nonnegative Least-Square

fit

Extracting Fitted Models

fitted

Fitted Matrix in NMF Models

foreach

Utilities and Extensions for Foreach Loops

gfile

Open a File Graphic Device

grid

Internal Grid Extension

heatmaps

Heatmaps of NMF Factors

inplace

Updating Objects In Place

lsNMF-nmf

Multiplicative Updates for LS-NMF

lverbose

Internal verbosity option

match_atrack

Extending Annotation Vectors

nmf

Running NMF algorithms

nmf-compare

Comparing Results from Different NMF Runs

nmf.equal

Testing Equality of NMF Models

nmfAlgorithm

Listing and Retrieving NMF Algorithms

nmfApply

Apply Function for NMF Objects

nmfCheck

Checking NMF Algorithm

nmfEstimateRank

Estimate Rank for NMF Models

nmfFormals

Showing Arguments of NMF Algorithms

nmfModel

Factory Methods NMF Models

nmfObject

Updating NMF Objects

nmfReport

Run NMF Methods and Generate a Report

nmfSeed

Seeding Strategies for NMF Algorithms

nmfWrapper

Wrapping NMF Algorithms

nmf_update_KL

NMF Multiplicative Updates for Kullback-Leibler Divergence

nmf_update_euclidean

NMF Multiplicative Updates for Euclidean Distance

nneg

Transforming from Mixed-sign to Nonnegative Data

nsNMF-nmf

NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).

objective-commaNMFfit-method

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.

offset-commaNMFOffset-method

Offsets in NMF Models with Offset

offset-commaNMFfit-method

Returns the offset from the fitted model.

offset-nmf

NMF Multiplicative Update for NMF with Offset Models

options

NMF Package Specific Options

parallel

Utilities for Parallel Computations

parse_formula

Simple Parsing of Formula

plot-commaNMFfit-commamissing-method

Plots the residual track computed at regular interval during the fit of the NMF model x.

predict

Clustering and Prediction

profplot

Plotting Expression Profiles

purity

Purity and Entropy of a Clustering

randomize

Randomizing Data

registry-algorithm

Registry for NMF Algorithms

residuals

Residuals in NMF Models

revPalette

Flags a Color Palette Specification for Reversion

rmatrix

Generating Random Matrices

rnmf

Generating Random NMF Models

rss

Residual Sum of Squares and Explained Variance

runtime-commaNMFList-method

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.

runtime.all-commaNMFfitXn-method

Returns the CPU time used to perform all the NMF fits stored in object.

scale.NMF

Rescaling NMF Models

scores

Feature Selection in NMF Models

seed

Interface for NMF Seeding Methods

setNMFMethod

Registering NMF Algorithms

setNMFSeed

NMFSeed is a constructor method that instantiate NMFSeed objects.