Man pages for NMF
Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

advancedAdvanced Usage of the Package NMF
aheatmapAnnotated Heatmaps
algorithm-commaNMFList-methodReturns the method names used to compute the NMF fits in the...
algorithmicGeneric Interface for Algorithms
assessAssessing and Comparing NMF Models
atrackAnnotation Tracks
basis-coef-methodsAccessing NMF Factors
basiscorCorrelations in NMF Models
biocSpecific NMF Layer for Bioconductor
canFitTesting Compatibility of Algorithm and Models
ccBreaksGenerate Break Intervals from Numeric Variables
c-commaNMF-methodConcatenating NMF Models
ccPaletteBuilds a Color Palette from Compact Color Specification
ccRampBuilds a Color Ramp from Compact Color Specification
ccSpecExtract Colour Palette Specification
checkErrorsError Checks in NMF Runs
cluster_matCluster Matrix Rows in Annotated Heatmaps
connectivityClustering Connectivity and Consensus Matrices
consensus-commaNMFfitX1-methodReturns the consensus matrix computed while performing all...
consensus-commaNMFfitXn-methodComputes the consensus matrix of the set of fits stored in...
consensushcHierarchical Clustering of a Consensus Matrix
cophcorCophenetic Correlation Coefficient
cutdendroFade Out the Upper Branches from a Dendrogram
devianceDistances and Objective Functions
dimnamesDimension names for NMF objects
dimsDimension of NMF Objects
dispersionDispersion of a Matrix
dot-fcnnlsInternal Routine for Fast Combinatorial Nonnegative...
esGolubGolub ExpressionSet
fcnnlsFast Combinatorial Nonnegative Least-Square
fitExtracting Fitted Models
fittedFitted Matrix in NMF Models
foreachUtilities and Extensions for Foreach Loops
Frobenius-nmfNMF Algorithm/Updates for Frobenius Norm
gfileOpen a File Graphic Device
gridInternal Grid Extension
heatmapsHeatmaps of NMF Factors
inplaceUpdating Objects In Place
isCRANcheckPackage Check Utils
KL-nmfNMF Algorithm/Updates for Kullback-Leibler Divergence
latexLaTeX Utilities for Vignettes
lsNMF-nmfMultiplicative Updates for LS-NMF
lverboseInternal verbosity option
match_atrackExtending Annotation Vectors
nmfRunning NMF algorithms
nmfAlgorithmListing and Retrieving NMF Algorithms
nmfApplyApply Function for NMF Objects
nmfCheckChecking NMF Algorithm
NMF-classGeneric Interface for Nonnegative Matrix Factorisation Models
nmf-compareComparing Results from Different NMF Runs
NMF-defunctDefunct Functions and Classes in the NMF Package
NMF-deprecatedDeprecated Functions in the Package NMF
nmf.equalTesting Equality of NMF Models
nmfEstimateRankEstimate Rank for NMF Models
NMFfit-classBase Class for to store Nonnegative Matrix Factorisation...
NMFfitXFactory Method for Multiple NMF Run Objects
NMFfitX1-classStructure for Storing the Best Fit Amongst Multiple NMF Runs
NMFfitX-classVirtual Class to Handle Results from Multiple Runs of NMF...
NMFfitXn-classStructure for Storing All Fits from Multiple NMF Runs
nmfFormalsShowing Arguments of NMF Algorithms
NMFList-classClass for Storing Heterogeneous NMF fits
nmfModelFactory Methods NMF Models
NMFns-classNMF Model - Nonsmooth Nonnegative Matrix Factorization
nmfObjectUpdating NMF Objects
NMFOffset-classNMF Model - Nonnegative Matrix Factorization with Offset
NMF-packageAlgorithms and framework for Nonnegative Matrix Factorization...
nmfReportRun NMF Methods and Generate a Report
nmfSeedSeeding Strategies for NMF Algorithms
NMFSeed-classBase class that defines the interface for NMF seeding...
NMFstd-classNMF Model - Standard model
NMFStrategyFactory Method for NMFStrategy Objects
NMFStrategy-classVirtual Interface for NMF Algorithms
NMFStrategyFunction-classInterface for Single Function NMF Strategies
NMFStrategyIterative-classInterface for Algorithms: Implementation for Iterative NMF...
nmf_update_euclideanNMF Multiplicative Updates for Euclidean Distance
nmf_update_KLNMF Multiplicative Updates for Kullback-Leibler Divergence
nmfWrapperWrapping NMF Algorithms
nnegTransforming from Mixed-sign to Nonnegative Data
nsNMF-nmfNMF Multiplicative Update for Nonsmooth Nonnegative Matrix...
objective-commaNMFfit-methodReturns the objective function associated with the algorithm...
offset-commaNMFfit-methodReturns the offset from the fitted model.
offset-commaNMFOffset-methodOffsets in NMF Models with Offset
offset-nmfNMF Multiplicative Update for NMF with Offset Models
optionsNMF Package Specific Options
parallelUtilities for Parallel Computations
parse_formulaSimple Parsing of Formula
plot-commaNMFfit-commamissing-methodPlots the residual track computed at regular interval during...
predictClustering and Prediction
profplotPlotting Expression Profiles
purityPurity and Entropy of a Clustering
randomizeRandomizing Data
registry-algorithmRegistry for NMF Algorithms
residualsResiduals in NMF Models
revPaletteFlags a Color Palette Specification for Reversion
rmatrixGenerating Random Matrices
RNGExtracting RNG Data from NMF Objects
rnmfGenerating Random NMF Models
rssResidual Sum of Squares and Explained Variance
runtime.all-commaNMFfitXn-methodReturns the CPU time used to perform all the NMF fits stored...
runtime-commaNMFList-methodReturns the CPU time required to compute all NMF fits in the...
scale.NMFRescaling NMF Models
scoresFeature Selection in NMF Models
seedInterface for NMF Seeding Methods
setNMFMethodRegistering NMF Algorithms
setNMFSeed'NMFSeed' is a constructor method that instantiate 'NMFSeed'...
setupComputational Setup Functions
show-commaNMFfit-methodShow method for objects of class 'NMFfit'
show-commaNMFfitX1-methodShow method for objects of class 'NMFfitX1'
show-commaNMFfitX-methodShow method for objects of class 'NMFfitX'
show-commaNMFfitXn-methodShow method for objects of class 'NMFfitXn'
show-commaNMFList-methodShow method for objects of class 'NMFList'
show-commaNMF-methodShow method for objects of class 'NMF'
show-commaNMFns-methodShow method for objects of class 'NMFns'
show-commaNMFOffset-methodShow method for objects of class 'NMFOffset'
show-commaNMFSeed-methodShow method for objects of class 'NMFSeed'
show-commaNMFStrategyIterative-methodShow method for objects of class 'NMFStrategyIterative'
silhouette.NMFSilhouette of NMF Clustering
smoothingSmoothing Matrix in Nonsmooth NMF Models
SNMF-nmfNMF Algorithm - Sparse NMF via Alternating NNLS
staticVarGet/Set a Static Variable in NMF Algorithms
stop-NMFStopping Criteria for NMF Iterative Strategies
Strategy-classGeneric Strategy Class
subset-NMFSub-setting NMF Objects
syntheticNMFSimulating Datasets
termsFixed Terms in NMF Models
terms-internalFixed Terms in NMF Models
t.NMFTransformation NMF Model Objects
txtProgressBarSimple Progress Bar
typesTesting NMF Objects
utilsUtility Function in the NMF Package
NMF documentation built on March 31, 2023, 6:55 p.m.