# Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

## Documentation for package ‘NMF’ version 0.25

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P R S T U W misc

NMF-package | Algorithms and framework for Nonnegative Matrix Factorization (NMF).

## -- A --

advanced-NMF | Advanced Usage of the Package NMF
aheatmap | Annotated Heatmaps
algorithm | Generic Interface for Algorithms
algorithm-method | Returns the method names used to compute the NMF fits in the list. It returns 'NULL' if the list is empty.
algorithm-method | Generic Interface for Algorithms
algorithm-methods | Generic Interface for Algorithms
algorithm<- | Generic Interface for Algorithms
algorithm<--method | Generic Interface for Algorithms
algorithm<--methods | Generic Interface for Algorithms
algorithmic-NMF | Generic Interface for Algorithms

## -- B --

basis | Accessing NMF Factors
basis-method | Accessing NMF Factors
basis-methods | Accessing NMF Factors
basis<- | Accessing NMF Factors
basis<--method | Accessing NMF Factors
basis<--methods | Accessing NMF Factors
basiscor | Correlations in NMF Models
basiscor-method | Correlations in NMF Models
basiscor-methods | Correlations in NMF Models
basismap | Heatmaps of NMF Factors
basismap-method | Heatmaps of NMF Factors
basismap-methods | Heatmaps of NMF Factors
basisnames | Dimension names for NMF objects
basisnames-method | Dimension names for NMF objects
basisnames-methods | Dimension names for NMF objects
basisnames<- | Dimension names for NMF objects
basisnames<--method | Dimension names for NMF objects
basisnames<--methods | Dimension names for NMF objects
bioc-NMF | Specific NMF Layer for Bioconductor
brunet-nmf | NMF Algorithm/Updates for Kullback-Leibler Divergence
brunet_R-nmf | NMF Algorithm/Updates for Kullback-Leibler Divergence
bterms | Fixed Terms in NMF Models

## -- C --

canFit | Testing Compatibility of Algorithm and Models
canFit-method | Testing Compatibility of Algorithm and Models
canFit-methods | Testing Compatibility of Algorithm and Models
coef | Accessing NMF Factors
coef-method | Accessing NMF Factors
coef-methods | Accessing NMF Factors
coef<- | Accessing NMF Factors
coef<--method | Accessing NMF Factors
coef<--methods | Accessing NMF Factors
coefficients | Accessing NMF Factors
coefficients-method | Accessing NMF Factors
coefficients-methods | Accessing NMF Factors
coefmap | Heatmaps of NMF Factors
coefmap-method | Heatmaps of NMF Factors
coefmap-methods | Heatmaps of NMF Factors
compare | Generic Interface for Algorithms
compare-method | Generic Interface for Algorithms
compare-method | Comparing Results from Different NMF Runs
compare-methods | Generic Interface for Algorithms
compare-NMF | Comparing Results from Different NMF Runs
connectivity | Clustering Connectivity and Consensus Matrices
connectivity-method | Clustering Connectivity and Consensus Matrices
connectivity-methods | Clustering Connectivity and Consensus Matrices
consensus | Clustering Connectivity and Consensus Matrices
consensus-method | Clustering Connectivity and Consensus Matrices
consensus-method | Returns the consensus matrix computed while performing all NMF runs, amongst which 'object' was selected as the best fit.
consensus-method | Computes the consensus matrix of the set of fits stored in 'object', as the mean connectivity matrix across runs.
consensus-methods | Clustering Connectivity and Consensus Matrices
consensushc | Hierarchical Clustering of a Consensus Matrix
consensushc-method | Hierarchical Clustering of a Consensus Matrix
consensushc-methods | Hierarchical Clustering of a Consensus Matrix
consensusmap | Heatmaps of NMF Factors
consensusmap-method | Heatmaps of NMF Factors
consensusmap-method | Comparing Results from Different NMF Runs
consensusmap-methods | Heatmaps of NMF Factors
cophcor | Cophenetic Correlation Coefficient
cophcor-method | Cophenetic Correlation Coefficient
cophcor-methods | Cophenetic Correlation Coefficient
cterms | Fixed Terms in NMF Models

## -- D --

deviance | Distances and Objective Functions
deviance-method | Distances and Objective Functions
deviance-methods | Distances and Objective Functions
dim-method | Dimension of NMF Objects
dim-NMF | Dimension of NMF Objects
dimnames-method | Dimension names for NMF objects
dimnames-NMF | Dimension names for NMF objects
dimnames<--method | Dimension names for NMF objects
dispersion | Dispersion of a Matrix
dispersion-method | Dispersion of a Matrix
dispersion-methods | Dispersion of a Matrix

## -- E --

entropy | Purity and Entropy of a Clustering
entropy-method | Purity and Entropy of a Clustering
entropy-methods | Purity and Entropy of a Clustering
esGolub | Golub ExpressionSet
evar | Residual Sum of Squares and Explained Variance
evar-method | Residual Sum of Squares and Explained Variance
evar-methods | Residual Sum of Squares and Explained Variance
existsNMFMethod | Registry for NMF Algorithms
existsNMFSeed | Seeding Strategies for NMF Algorithms
extractFeatures | Feature Selection in NMF Models
extractFeatures-method | Feature Selection in NMF Models
extractFeatures-methods | Feature Selection in NMF Models

## -- F --

fcnnls | Fast Combinatorial Nonnegative Least-Square
fcnnls-method | Fast Combinatorial Nonnegative Least-Square
fcnnls-methods | Fast Combinatorial Nonnegative Least-Square
featureNames-method | Specific NMF Layer for Bioconductor
featureNames<--method | Specific NMF Layer for Bioconductor
featureScore | Feature Selection in NMF Models
featureScore-method | Feature Selection in NMF Models
featureScore-methods | Feature Selection in NMF Models
fit | Extracting Fitted Models
fit-method | Extracting Fitted Models
fit-methods | Extracting Fitted Models
fit<- | Extracting Fitted Models
fit<--method | Extracting Fitted Models
fit<--methods | Extracting Fitted Models
fitted | Fitted Matrix in NMF Models
fitted-method | Fitted Matrix in NMF Models
fitted-methods | Fitted Matrix in NMF Models
Frobenius-nmf | NMF Algorithm/Updates for Frobenius Norm

## -- G --

getNMFMethod | Registry for NMF Algorithms
getNMFSeed | Seeding Strategies for NMF Algorithms
getRNG1 | Extracting RNG Data from NMF Objects
getRNG1-method | Extracting RNG Data from NMF Objects
getRNG1-methods | Extracting RNG Data from NMF Objects
gVariable | Utilities for Parallel Computations

## -- H --

hasBasis | Testing NMF Objects
hasCoef | Testing NMF Objects
hasTrack | Residuals in NMF Models
heatmap-NMF | Heatmaps of NMF Factors
hostfile | Utilities for Parallel Computations

## -- I --

ibasis | Fixed Terms in NMF Models
ibterms | Fixed Terms in NMF Models
ibterms-method | Fixed Terms in NMF Models
ibterms-methods | Fixed Terms in NMF Models
icoef | Fixed Terms in NMF Models
icterms | Fixed Terms in NMF Models
icterms-method | Fixed Terms in NMF Models
icterms-methods | Fixed Terms in NMF Models
initialize-method | NMF Model - Nonnegative Matrix Factorization with Offset
is.empty.nmf | Testing NMF Objects
is.nmf | Testing NMF Objects
is.partial.nmf | Testing NMF Objects
isCHECK | Package Check Utils
isCRANcheck | Package Check Utils
isNMFfit | Testing NMF Objects
iterms | Fixed Terms in NMF Models

## -- K --

KL-nmf | NMF Algorithm/Updates for Kullback-Leibler Divergence

## -- L --

latex_bibliography | LaTeX Utilities for Vignettes
latex_preamble | LaTeX Utilities for Vignettes
lee-nmf | NMF Algorithm/Updates for Frobenius Norm
lee_R-nmf | NMF Algorithm/Updates for Frobenius Norm
loadings-method | Accessing NMF Factors
logs | Generic Interface for Algorithms
logs-method | Generic Interface for Algorithms
logs-methods | Generic Interface for Algorithms
lsNMF-nmf | Multiplicative Updates for LS-NMF

## -- M --

match_atrack | Extending Annotation Vectors
metagenes | Specific NMF Layer for Bioconductor
metagenes<- | Specific NMF Layer for Bioconductor
metaHeatmap | Defunct Functions and Classes in the NMF Package
metaHeatmap-method | Defunct Functions and Classes in the NMF Package
metaHeatmap-methods | Defunct Functions and Classes in the NMF Package
metaprofiles | Specific NMF Layer for Bioconductor
metaprofiles<- | Specific NMF Layer for Bioconductor
methods-NMF | Registry for NMF Algorithms
minfit | Extracting Fitted Models
minfit-method | Extracting Fitted Models
minfit-methods | Extracting Fitted Models
misc | Generic Interface for Nonnegative Matrix Factorisation Models
modelname | Generic Interface for Algorithms
modelname-method | Generic Interface for Algorithms
modelname-methods | Generic Interface for Algorithms

## -- N --

nbasis | Dimension of NMF Objects
nbasis-method | Dimension of NMF Objects
nbasis-methods | Dimension of NMF Objects
nbterms | Fixed Terms in NMF Models
ncterms | Fixed Terms in NMF Models
niter | Generic Interface for Algorithms
niter-method | Generic Interface for Algorithms
niter-methods | Generic Interface for Algorithms
niter<- | Generic Interface for Algorithms
niter<--method | Generic Interface for Algorithms
niter<--methods | Generic Interface for Algorithms
nmeta | Specific NMF Layer for Bioconductor
NMF | Algorithms and framework for Nonnegative Matrix Factorization (NMF).
nmf | Running NMF algorithms
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-method | Specific NMF Layer for Bioconductor
nmf-method | Running NMF algorithms
nmf-methods | Running NMF algorithms
nmf.equal | Testing Equality of NMF Models
nmf.equal-method | Testing Equality of NMF Models
nmf.equal-methods | Testing Equality of NMF Models
nmf.getOption | NMF Package Specific Options
nmf.options | NMF Package Specific Options
nmf.printOptions | NMF Package Specific Options
nmf.resetOptions | NMF Package Specific Options
nmf.stop.connectivity | Stopping Criteria for NMF Iterative Strategies
nmf.stop.iteration | Stopping Criteria for NMF Iterative Strategies
nmf.stop.stationary | Stopping Criteria for NMF Iterative Strategies
nmf.stop.threshold | Stopping Criteria for NMF Iterative Strategies
nmfAlgorithm | Listing and Retrieving NMF Algorithms
nmfAlgorithm.brunet | NMF Algorithm/Updates for Kullback-Leibler Divergence
nmfAlgorithm.brunet_R | NMF Algorithm/Updates for Kullback-Leibler Divergence
nmfAlgorithm.Frobenius | NMF Algorithm/Updates for Frobenius Norm
nmfAlgorithm.KL | NMF Algorithm/Updates for Kullback-Leibler Divergence
nmfAlgorithm.lee | NMF Algorithm/Updates for Frobenius Norm
nmfAlgorithm.lee_R | NMF Algorithm/Updates for Frobenius Norm
nmfAlgorithm.lsNMF | Multiplicative Updates for LS-NMF
nmfAlgorithm.nsNMF | NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
nmfAlgorithm.nsNMF_R | NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
nmfAlgorithm.offset | NMF Multiplicative Update for NMF with Offset Models
nmfAlgorithm.offset_R | NMF Multiplicative Update for NMF with Offset Models
nmfAlgorithm.SNMF_L | NMF Algorithm - Sparse NMF via Alternating NNLS
nmfAlgorithm.SNMF_R | NMF Algorithm - Sparse NMF via Alternating NNLS
nmfApply | Apply Function for NMF Objects
nmfArgs | Showing Arguments of NMF Algorithms
nmfCheck | Checking NMF Algorithm
nmfDistance | Distances and Objective Functions
nmfEstimateRank | Estimate Rank for NMF Models
NMFfit | Base Class for to store Nonnegative Matrix Factorisation results
NMFfit-class | Base Class for to store Nonnegative Matrix Factorisation results
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
nmfFormals | Showing Arguments of NMF Algorithms
NMFList-class | Class for Storing Heterogeneous NMF fits
nmfModel | Factory Methods NMF Models
nmfModel-method | Specific NMF Layer for Bioconductor
nmfModel-method | Factory Methods NMF Models
nmfModel-methods | Factory Methods NMF Models
nmfModels | Factory Methods NMF Models
NMFns-class | NMF Model - Nonsmooth Nonnegative Matrix Factorization
nmfObject | Updating NMF Objects
NMFOffset-class | NMF Model - Nonnegative Matrix Factorization with Offset
nmfRegisterAlgorithm | Registering NMF Algorithms
nmfReport | Run NMF Methods and Generate a Report
NMFSeed | 'NMFSeed' is a constructor method that instantiate 'NMFSeed' objects.
nmfSeed | Seeding Strategies for NMF Algorithms
NMFSeed-class | Base class that defines the interface for NMF seeding methods.
NMFSeed-method | 'NMFSeed' is a constructor method that instantiate 'NMFSeed' objects.
NMFSeed-methods | 'NMFSeed' is a constructor method that instantiate 'NMFSeed' objects.
NMFstd-class | NMF Model - Standard model
NMFStop | Stopping Criteria for NMF Iterative Strategies
NMFStrategy | Factory Method for NMFStrategy Objects
NMFStrategy-method | Factory Method for NMFStrategy Objects
NMFStrategy-methods | Factory Method for NMFStrategy Objects
NMFStrategyFunction-class | Interface for Single Function NMF Strategies
NMFStrategyIterative-class | Interface for Algorithms: Implementation for Iterative NMF Algorithms
nmf_update.brunet | NMF Algorithm/Updates for Kullback-Leibler Divergence
nmf_update.brunet_R | NMF Algorithm/Updates for Kullback-Leibler Divergence
nmf_update.euclidean | NMF Multiplicative Updates for Euclidean Distance
nmf_update.euclidean.h | NMF Multiplicative Updates for Euclidean Distance
nmf_update.euclidean.h_R | NMF Multiplicative Updates for Euclidean Distance
nmf_update.euclidean.w | NMF Multiplicative Updates for Euclidean Distance
nmf_update.euclidean.w_R | NMF Multiplicative Updates for Euclidean Distance
nmf_update.euclidean_offset.h | NMF Multiplicative Update for NMF with Offset Models
nmf_update.euclidean_offset.w | NMF Multiplicative Update for NMF with Offset Models
nmf_update.KL | NMF Multiplicative Updates for Kullback-Leibler Divergence
nmf_update.KL.h | NMF Multiplicative Updates for Kullback-Leibler Divergence
nmf_update.KL.h_R | NMF Multiplicative Updates for Kullback-Leibler Divergence
nmf_update.KL.w | NMF Multiplicative Updates for Kullback-Leibler Divergence
nmf_update.KL.w_R | NMF Multiplicative Updates for Kullback-Leibler Divergence
nmf_update.lee | NMF Algorithm/Updates for Frobenius Norm
nmf_update.lee_R | NMF Algorithm/Updates for Frobenius Norm
nmf_update.lsnmf | Multiplicative Updates for LS-NMF
nmf_update.ns | NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
nmf_update.ns_R | NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
nmf_update.offset | NMF Multiplicative Update for NMF with Offset Models
nmf_update.offset_R | NMF Multiplicative Update for NMF with Offset Models
nneg | Transforming from Mixed-sign to Nonnegative Data
nneg-method | Specific NMF Layer for Bioconductor
nneg-method | Transforming from Mixed-sign to Nonnegative Data
nneg-methods | Transforming from Mixed-sign to Nonnegative Data
nrun | Generic Interface for Algorithms
nrun-method | Generic Interface for Algorithms
nrun-methods | Generic Interface for Algorithms
nsNMF_R-nmf | NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
nterms | Fixed Terms in NMF Models

## -- O --

objective | Generic Interface for Algorithms
objective-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.
objective-methods | Generic Interface for Algorithms
objective<- | Generic Interface for Algorithms
objective<--method | Generic Interface for Algorithms
objective<--methods | Generic Interface for Algorithms
offset-method | Offsets in NMF Models with Offset
offset-method | Returns the offset from the fitted model.
offset_R-nmf | NMF Multiplicative Update for NMF with Offset Models
options-NMF | NMF Package Specific Options

## -- P --

parallel-NMF | Utilities for Parallel Computations
plot-method | Comparing Results from Different NMF Runs
plot-method | Plots the residual track computed at regular interval during the fit of the NMF model 'x'.
plot.NMF.consensus | Computes the consensus matrix of the set of fits stored in 'object', as the mean connectivity matrix across runs.
plot.NMF.rank | Estimate Rank for NMF Models
posneg | Transforming from Mixed-sign to Nonnegative Data
predict | Clustering and Prediction
predict-method | Clustering and Prediction
predict-methods | Clustering and Prediction
profcor | Correlations in NMF Models
profcor-method | Correlations in NMF Models
profcor-methods | Correlations in NMF Models
profplot | Plotting Expression Profiles
profplot.default | Plotting Expression Profiles
purity | Purity and Entropy of a Clustering
purity-method | Purity and Entropy of a Clustering
purity-methods | Purity and Entropy of a Clustering

## -- R --

randomize | Randomizing Data
removeNMFMethod | Registry for NMF Algorithms
removeNMFSeed | 'NMFSeed' is a constructor method that instantiate 'NMFSeed' objects.
residuals | Residuals in NMF Models
residuals-method | Residuals in NMF Models
residuals-methods | Residuals in NMF Models
residuals<- | Residuals in NMF Models
residuals<--method | Residuals in NMF Models
residuals<--methods | Residuals in NMF Models
rmatrix | Generating Random Matrices
rmatrix-method | Generating Random Matrices
rmatrix-methods | Generating Random Matrices
rnmf | Generating Random NMF Models
rnmf-method | Specific NMF Layer for Bioconductor
rnmf-method | Generating Random NMF Models
rnmf-methods | Generating Random NMF Models
rposneg | Transforming from Mixed-sign to Nonnegative Data
rposneg-method | Specific NMF Layer for Bioconductor
rposneg-method | Transforming from Mixed-sign to Nonnegative Data
rposneg-methods | Transforming from Mixed-sign to Nonnegative Data
rss | Residual Sum of Squares and Explained Variance
rss-method | Residual Sum of Squares and Explained Variance
rss-methods | Residual Sum of Squares and Explained Variance
run | Generic Interface for Algorithms
run-method | Factory Method for NMFStrategy Objects
run-method | Specific NMF Layer for Bioconductor
run-methods | Generic Interface for Algorithms
runtime | Generic Interface for Algorithms
runtime-method | Generic Interface for Algorithms
runtime-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-methods | Generic Interface for Algorithms
runtime.all | Generic Interface for Algorithms
runtime.all-method | Generic Interface for Algorithms
runtime.all-method | Returns the CPU time used to perform all the NMF fits stored in 'object'.
runtime.all-methods | Generic Interface for Algorithms

## -- S --

sampleNames-method | Specific NMF Layer for Bioconductor
sampleNames<--method | Specific NMF Layer for Bioconductor
scale.NMF | Rescaling NMF Models
scoef | Accessing NMF Factors
scoef-method | Accessing NMF Factors
scoef-methods | Accessing NMF Factors
seed | Interface for NMF Seeding Methods
seed-method | Specific NMF Layer for Bioconductor
seed-method | Interface for NMF Seeding Methods
seed-methods | Interface for NMF Seeding Methods
seeding | Generic Interface for Algorithms
seeding-method | Generic Interface for Algorithms
seeding-methods | Generic Interface for Algorithms
seeding<- | Generic Interface for Algorithms
seeding<--method | Generic Interface for Algorithms
seeding<--methods | Generic Interface for Algorithms
selectNMFMethod | Registry for NMF Algorithms
seqtime | Generic Interface for Algorithms
seqtime-method | Generic Interface for Algorithms
seqtime-methods | Generic Interface for Algorithms
setNMFMethod | Registering NMF Algorithms
setNMFSeed | 'NMFSeed' is a constructor method that instantiate 'NMFSeed' objects.
setupBackend | Computational Setup Functions
setupLibPaths | Computational Setup Functions
setupRNG | Computational Setup Functions
setupSharedMemory | Computational Setup Functions
setupTempDirectory | Computational Setup Functions
show-method | Show method for objects of class 'NMF'
show-method | Show method for objects of class 'NMFList'
show-method | Show method for objects of class 'NMFOffset'
show-method | Show method for objects of class 'NMFSeed'
show-method | Show method for objects of class 'NMFStrategyIterative'
show-method | Show method for objects of class 'NMFfit'
show-method | Show method for objects of class 'NMFfitX'
show-method | Show method for objects of class 'NMFfitX1'
show-method | Show method for objects of class 'NMFfitXn'
show-method | Show method for objects of class 'NMFns'
silhouette.NMF | Silhouette of NMF Clustering
smoothing | Smoothing Matrix in Nonsmooth NMF Models
SNMF/L-nmf | NMF Algorithm - Sparse NMF via Alternating NNLS
SNMF/R-nmf | NMF Algorithm - Sparse NMF via Alternating NNLS
sparseness | Sparseness
sparseness-method | Sparseness
sparseness-methods | Sparseness
staticVar | Get/Set a Static Variable in NMF Algorithms
stop-NMF | Stopping Criteria for NMF Iterative Strategies
str_args | Utility Function in the NMF Package
summary | Assessing and Comparing NMF Models
summary-method | Assessing and Comparing NMF Models
summary-method | Comparing Results from Different NMF Runs
summary-methods | Assessing and Comparing NMF Models
summary-NMF | Assessing and Comparing NMF Models
syntheticNMF | Simulating Datasets

## -- T --

t.NMF | Transformation NMF Model Objects
trackError | Residuals in NMF Models
ts_eval | Utilities for Parallel Computations
ts_tempfile | Utilities for Parallel Computations

## -- U --

utils-NMF | Utility Function in the NMF Package

## -- W --

which.best | Advanced Usage of the Package NMF
wrss | Multiplicative Updates for LS-NMF

## -- misc --

$-method | Generic Interface for Nonnegative Matrix Factorisation Models
$<--method | Generic Interface for Nonnegative Matrix Factorisation Models
.atrack-method | Specific NMF Layer for Bioconductor
.basis | Accessing NMF Factors
.basis-method | Accessing NMF Factors
.basis-methods | Accessing NMF Factors
.basis<- | Accessing NMF Factors
.basis<--method | Accessing NMF Factors
.basis<--methods | Accessing NMF Factors
.coef | Accessing NMF Factors
.coef-method | Accessing NMF Factors
.coef-methods | Accessing NMF Factors
.coef<- | Accessing NMF Factors
.coef<--method | Accessing NMF Factors
.coef<--methods | Accessing NMF Factors
.DollarNames-method | Generic Interface for Nonnegative Matrix Factorisation Models
.fcnnls | Internal Routine for Fast Combinatorial Nonnegative Least-Squares
.getRNG | Extracting RNG Data from NMF Objects
.getRNG-method | Extracting RNG Data from NMF Objects
.getRNG-methods | Extracting RNG Data from NMF Objects
[-method | Sub-setting NMF Objects