Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

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Documentation for package ‘NMF’ version 0.28

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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
aggregate.measure Utility function to aggregate numerical quality measures from 'NMFfitXn' objects.
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