Documentation

• advanced-NMF(which.best)
  Advanced Usage of the Package NMF
• aheatmap
  Annotated Heatmaps
• algorithmic-NMF(algorithm, algorithm<-, algorithm<--methods, algorithm-methods, algorithm<-,NMFfit,ANY-method, algorithm,NMFfit-method, algorithm,NMFfitXn-method, algorithm<-,NMFSeed,function-method, algorithm,NMFSeed-method, algorithm<-,NMFStrategyFunction,function-method, algorithm,NMFStrategyFunction-method, algorithm<-,NMFStrategyOctave,character-method, compare, compare-methods, compare,NMFfitXn-method, logs, logs,ANY-method, logs-methods, modelname, modelname,ANY-method, modelname-methods, modelname,NMFfit-method, modelname,NMFfitXn-method, modelname,NMFStrategy-method, niter, niter<-, niter<--methods, niter-methods, niter,NMFfit-method, niter<-,NMFfit,numeric-method, nrun, nrun,ANY-method, nrun-methods, nrun,NMFfit-method, nrun,NMFfitX1-method, nrun,NMFfitX-method, nrun,NMFfitXn-method, objective, objective<-, objective<--methods, objective-methods, objective<-,NMFfit,ANY-method, run, run-methods, runtime, runtime.all, runtime.all-methods, runtime.all,NMFfit-method, runtime.all,NMFfitX-method, runtime-methods, runtime,NMFfit-method, seeding, seeding<-, seeding<--methods, seeding-methods, seeding<-,NMFfit-method, seeding,NMFfit-method, seeding,NMFfitXn-method, seqtime, seqtime-methods, seqtime,NMFfitXn-method, seqtime,NMFList-method)
  Generic Interface for Algorithms
• algorithm,NMFList-method
  Returns the method names used to compute the NMF fits in the list.
• algorithm,NMFStrategyOctave-method
  Returns the name of the Octave/Matlab function that implements the NMF algorithm -- as stored in
• basis(.basis, .basis<-, basis<-, basis<-,ANY-method, basis,ANY-method, .basis<--methods, .basis-methods, basis<--methods, basis-methods, .basis<-,NMFfit,matrix-method, .basis,NMFfit-method, basis,NMFfitXn-method, .basis<-,NMF,matrix-method, .basis,NMF-method, basis,NMF-method, .basis<-,NMFstd,matrix-method, .basis,NMFstd-method, coef, .coef, .coef<-, coef<-, coef<-,ANY-method, coefficients, coefficients-methods, coefficients,NMF-method, .coef<--methods, .coef-methods, coef<--methods, coef-methods, .coef<-,NMFfit,matrix-method, .coef,NMFfit-method, coef,NMFfitXn-method, .coef<-,NMF,matrix-method, .coef,NMF-method, coef,NMF-method, .coef<-,NMFstd,matrix-method, .coef,NMFstd-method, loadings,NMF-method, scoef, scoef,matrix-method, scoef-methods, scoef,NMF-method)
  Accessing NMF Factors
• basiscor(basiscor,matrix,NMF-method, basiscor-methods, basiscor,NMF,matrix-method, basiscor,NMF,missing-method, basiscor,NMF,NMF-method, profcor, profcor,matrix,NMF-method, profcor-methods, profcor,NMF,matrix-method, profcor,NMF,missing-method, profcor,NMF,NMF-method)
  Correlations in NMF Models
• basisnames(basisnames<-, basisnames<-,ANY-method, basisnames,ANY-method, basisnames<--methods, basisnames-methods, dimnames-NMF, dimnames<-,NMF-method, dimnames,NMF-method)
  Dimension names for NMF objects
• bioc-NMF(.atrack,ExpressionSet-method, featureNames,NMFfitX-method, featureNames<-,NMF-method, featureNames,NMF-method, metagenes, metagenes<-, metaprofiles, metaprofiles<-, nmeta, nmf,ExpressionSet,ANY,ANY-method, nmf,matrix,ExpressionSet,ANY-method, nmfModel,ANY,ExpressionSet-method, nmfModel,ExpressionSet,ANY-method, nneg,ExpressionSet-method, rnmf,ANY,ExpressionSet-method, rposneg,ExpressionSet-method, run,NMFStrategy,ExpressionSet,ANY-method, sampleNames<-,NMF,ANY-method, sampleNames,NMFfitX-method, sampleNames,NMF-method, seed,ExpressionSet,ANY,ANY-method)
  Specific NMF Layer for Bioconductor
• canFit(canFit,character,ANY-method, canFit-methods, canFit,NMFStrategy,character-method, canFit,NMFStrategy,NMF-method)
  Testing Compatibility of Algorithm and Models
• compare-NMF(compare,list-method, compare,NMFfit-method, consensusmap,list-method, consensusmap,NMF.rank-method, plot,NMFList,missing-method, summary,NMFList-method)
  Comparing Results from Different NMF Runs
• connectivity(connectivity,ANY-method, connectivity,factor-method, connectivity-methods, connectivity,NMF-method, connectivity,numeric-method, consensus, consensus-methods, consensus,NMFfitX-method, consensus,NMF-method)
  Clustering Connectivity and Consensus Matrices
• consensushc(consensushc,matrix-method, consensushc-methods, consensushc,NMFfitX-method, consensushc,NMF-method)
  Hierarchical Clustering of a Consensus Matrix
• consensus,NMFfitX1-method
  Returns the consensus matrix computed while performing all NMF runs,
• consensus,NMFfitXn-method(plot.NMF.consensus)
  Computes the consensus matrix of the set of fits stored in
• cophcor(cophcor,matrix-method, cophcor-methods, cophcor,NMFfitX-method)
  Cophenetic Correlation Coefficient
• deviance(deviance-methods, deviance,NMFfit-method, deviance,NMFfitX-method, deviance,NMF-method, deviance,NMFStrategy-method, nmfDistance)
  Distances and Objective Functions
• dispersion(dispersion,matrix-method, dispersion-methods, dispersion,NMFfitX-method)
  Dispersion of a Matrix
• esGolub
  Golub ExpressionSet
• fcnnls(fcnnls,ANY,numeric-method, fcnnls,matrix,matrix-method, fcnnls-methods, fcnnls,numeric,matrix-method)
  Fast Combinatorial Nonnegative Least-Square
• .fcnnls
  Internal Routine for Fast Combinatorial Nonnegative Least-Squares
• featureScore(extractFeatures, extractFeatures,matrix-method, extractFeatures-methods, extractFeatures,NMF-method, featureScore,matrix-method, featureScore-methods, featureScore,NMF-method)
  Feature Selection in NMF Models
• fit(fit<-, fit<--methods, fit-methods, fit,NMFfit-method, fit<-,NMFfit,NMF-method, fit,NMFfitX1-method, fit,NMFfitX-method, fit,NMFfitXn-method, minfit, minfit-methods, minfit,NMFfit-method, minfit,NMFfitX1-method, minfit,NMFfitX-method, minfit,NMFfitXn-method)
  Extracting Fitted Models
• fitted(fitted-methods, fitted,NMFfit-method, fitted,NMF-method, fitted,NMFns-method, fitted,NMFOffset-method, fitted,NMFstd-method)
  Fitted Matrix in NMF Models
• getRNG1(.getRNG, getRNG1-methods, getRNG1,NMFfitX1-method, getRNG1,NMFfitX-method, getRNG1,NMFfitXn-method, .getRNG-methods, .getRNG,NMFfitXn-method)
  Extracting RNG Data from NMF Objects
• heatmap-NMF(basismap, basismap-methods, basismap,NMFfitX-method, basismap,NMF-method, coefmap, coefmap-methods, coefmap,NMFfitX-method, coefmap,NMF-method, consensusmap, consensusmap,matrix-method, consensusmap-methods, consensusmap,NMFfitX-method, consensusmap,NMF-method)
  Heatmaps of NMF Factors
• ibterms(bterms, cterms, ibasis, ibterms-methods, ibterms,NMFfit-method, ibterms,NMFfitX-method, ibterms,NMF-method, ibterms,NMFstd-method, icoef, icterms, icterms-methods, icterms,NMFfit-method, icterms,NMF-method, icterms,NMFstd-method, iterms, nbterms, ncterms, nterms)
  Fixed Terms in NMF Models
• is.nmf(hasBasis, hasCoef, is.empty.nmf, isNMFfit, is.partial.nmf)
  Testing NMF Objects
• match_atrack
  Extending Annotation Vectors
• methods-NMF(existsNMFMethod, getNMFMethod, removeNMFMethod, selectNMFMethod)
  Registry for NMF Algorithms
• nbasis(dim-NMF, dim,NMFfitXn-method, dim,NMF-method, nbasis,ANY-method, nbasis-methods, nbasis,NMFfitXn-method)
  Dimension of NMF Objects
• nmf(nmf,data.frame,ANY,ANY-method, nmf,formula,ANY,ANY-method, nmf,matrix,data.frame,ANY-method, nmf,matrix,matrix,ANY-method, nmf,matrix,missing,ANY-method, nmf,matrix,NMF,ANY-method, nmf,matrix,NULL,ANY-method, nmf,matrix,numeric,character-method, nmf,matrix,numeric,function-method, nmf,matrix,numeric,list-method, nmf,matrix,numeric,missing-method, nmf,matrix,numeric,NMFStrategy-method, nmf,matrix,numeric,NULL-method, nmf-methods)
  Running NMF algorithms
• nmfAlgorithm
  Listing and Retrieving NMF Algorithms
• nmfAlgorithm.SNMF_R(nmfAlgorithm.SNMF_L, SNMF/L-nmf, SNMF/R-nmf)
  NMF Algorithm - Sparse NMF via Alternating NNLS
• nmfApply
  Apply Function for NMF Objects
• nmfCheck
  Checking NMF Algorithm
• NMF-class(.DollarNames,NMF-method, misc, $<-,NMF-method, $,NMF-method)
  Generic Interface for Nonnegative Matrix Factorisation Models
• NMF-defunct(metaHeatmap, metaHeatmap,matrix-method, metaHeatmap-methods, metaHeatmap,NMFfitX-method, metaHeatmap,NMF-method)
  Defunct Functions and Classes in the NMF Package
• NMF-deprecated
  Deprecated Functions in the Package NMF
• nmf.equal(nmf.equal,list,list-method, nmf.equal,list,missing-method, nmf.equal-methods, nmf.equal,NMFfit,NMFfit-method, nmf.equal,NMFfit,NMF-method, nmf.equal,NMFfitX1,NMFfitX1-method, nmf.equal,NMFfitX,NMF-method, nmf.equal,NMF,NMFfit-method, nmf.equal,NMF,NMFfitX-method, nmf.equal,NMF,NMF-method)
  Testing Equality of NMF Models
• nmfEstimateRank(plot.NMF.rank)
  Estimate Rank for NMF Models
• NMFfit-class(NMFfit)
  Base Class for to store Nonnegative Matrix Factorisation results
• NMFfitX1-class
  Structure for Storing the Best Fit Amongst Multiple NMF Runs
• NMFfitX-class
  Virtual Class to Handle Results from Multiple Runs of NMF Algorithms
• NMFfitXn-class
  Structure for Storing All Fits from Multiple NMF Runs
• nmfFormals(nmfArgs)
  Showing Arguments of NMF Algorithms
• NMFList-class
  Class for Storing Heterogeneous NMF fits
• [,NMF-method
  Sub-setting NMF Objects
• nmfModel(nmfModel,data.frame,data.frame-method, nmfModel,formula,ANY-method, nmfModel,matrix,ANY-method, nmfModel,matrix,matrix-method, nmfModel-methods, nmfModel,missing,ANY-method, nmfModel,missing,missing-method, nmfModel,NULL,ANY-method, nmfModel,numeric,matrix-method, nmfModel,numeric,missing-method, nmfModel,numeric,numeric-method, nmfModels)
  Factory Methods NMF Models
• NMFns-class
  NMF Model - Nonsmooth Nonnegative Matrix Factorization
• nmfObject
  Updating NMF Objects
• NMFOffset-class(initialize,NMFOffset-method)
  NMF Model - Nonnegative Matrix Factorization with Offset
• NMF-package(NMF)
  Algorithms and framework for Nonnegative Matrix Factorization (NMF).
• nmfSeed(existsNMFSeed, getNMFSeed)
  Seeding Strategies for NMF Algorithms
• NMFSeed(NMFSeed,character-method, NMFSeed-methods, NMFSeed,NMFSeed-method, removeNMFSeed, setNMFSeed)
  NMFSeed
• NMFSeed-class
  Base class that defines the interface for NMF seeding methods.
• NMFstd-class
  NMF Model - Standard model
• NMFStop(nmf.stop.connectivity, nmf.stop.iteration, nmf.stop.stationary, nmf.stop.threshold, stop-NMF)
  Stopping Criteria for NMF Iterative Strategies
• NMFStrategy(NMFStrategy,character,character-method, NMFStrategy,character,function-method, NMFStrategy,character,missing-method, NMFStrategy,character,NMFStrategy-method, NMFStrategy-methods, NMFStrategy,missing,character-method, NMFStrategy,NMFStrategy,missing-method, NMFStrategy,NULL,character-method, NMFStrategy,NULL,NMFStrategy-method, run,NMFStrategyFunction,matrix,NMFfit-method, run,NMFStrategyIterative,matrix,NMFfit-method, run,NMFStrategyIterativeX,matrix,NMFfit-method, run,NMFStrategy,matrix,NMFfit-method, run,NMFStrategy,matrix,NMF-method, run,NMFStrategyOctave,matrix,NMFfit-method)
  Factory Method for NMFStrategy Objects
• NMFStrategyFunction-class
  Interface for Single Function NMF Strategies
• NMFStrategyIterative-class
  Interface for Algorithms: Implementation for Iterative NMF Algorithms
• NMFStrategyOctave-class(show,NMFStrategyOctave-method)
  S4 Interface for Octave-Matlab NMF Algorithms
• nmf_update.brunet_R(brunet_M-nmf, brunet-nmf, brunet_R-nmf, KL-nmf, nmfAlgorithm.brunet, nmfAlgorithm.brunet_M, nmfAlgorithm.brunet_R, nmfAlgorithm.KL, nmf_update.brunet)
  NMF Algorithm/Updates for Kullback-Leibler Divergence
• nmf_update.euclidean.h(nmf_update.euclidean, nmf_update.euclidean.h_R, nmf_update.euclidean.w, nmf_update.euclidean.w_R)
  NMF Multiplicative Updates for Euclidean Distance
• nmf_update.euclidean_offset.h(nmfAlgorithm.offset, nmfAlgorithm.offset_R, nmf_update.euclidean_offset.w, nmf_update.offset, nmf_update.offset_R, offset_R-nmf)
  NMF Multiplicative Update for NMF with Offset Models
• nmf_update.KL.h(nmf_update.KL, nmf_update.KL.h_R, nmf_update.KL.w, nmf_update.KL.w_R)
  NMF Multiplicative Updates for Kullback-Leibler Divergence
• nmf_update.lee_R(Frobenius-nmf, lee-nmf, lee_R-nmf, nmfAlgorithm.Frobenius, nmfAlgorithm.lee, nmfAlgorithm.lee_R, nmf_update.lee)
  NMF Algorithm/Updates for Frobenius Norm
• nmf_update.lsnmf(lsNMF-nmf, nmfAlgorithm.lsNMF, wrss)
  Multiplicative Updates for LS-NMF
• nmf_update.ns(nmfAlgorithm.nsNMF, nmfAlgorithm.nsNMF_R, nmf_update.ns_R, nsNMF_R-nmf)
  NMF Multiplicative Update for Nonsmooth Nonnegative Matrix Factorization (nsNMF).
• nneg(nneg,matrix-method, nneg-methods, nneg,NMF-method, posneg, rposneg, rposneg,matrix-method, rposneg-methods, rposneg,NMF-method)
  Transforming from Mixed-sign to Nonnegative Data
• objective,NMFfit-method
  Returns the objective function associated with the algorithm that computed the
• offset,NMFfit-method
  Returns the offset from the fitted model.
• offset,NMFOffset-method
  Offsets in NMF Models with Offset
• options-NMF(nmf.getOption, nmf.options, nmf.printOptions, nmf.resetOptions)
  NMF Package Specific Options
• parallel-NMF(gVariable, hostfile, ts_eval, ts_tempfile)
  Utilities for Parallel Computations
• plot,NMFfit,missing-method
  Plots the residual track computed at regular interval during the fit of
• predict(predict-methods, predict,NMFfitX-method, predict,NMF-method)
  Clustering and Prediction
• profplot(profplot.default)
  Plotting Expression Profiles
• purity(entropy, entropy,ANY,ANY-method, entropy,factor,ANY-method, entropy-methods, entropy,NMFfitXn,ANY-method, entropy,table,missing-method, purity,ANY,ANY-method, purity,factor,ANY-method, purity-methods, purity,NMFfitXn,ANY-method, purity,table,missing-method)
  Purity and Entropy of a Clustering
• randomize
  Randomizing Data
• residuals(hasTrack, residuals<-, residuals<--methods, residuals-methods, residuals<-,NMFfit-method, residuals,NMFfit-method, residuals,NMFfitX-method, trackError)
  Residuals in NMF Models
• rmatrix(rmatrix,ANY-method, rmatrix-methods, rmatrix,NMF-method, rmatrix,numeric-method)
  Generating Random Matrices
• rnmf(rnmf,ANY,data.frame-method, rnmf,ANY,matrix-method, rnmf,formula,ANY-method, rnmf-methods, rnmf,missing,missing-method, rnmf,NMF,missing-method, rnmf,NMF,numeric-method, rnmf,NMFOffset,numeric-method, rnmf,numeric,missing-method, rnmf,numeric,numeric-method)
  Generating Random NMF Models
• rss(evar, evar,ANY-method, evar-methods, rss,ANY-method, rss,matrix-method, rss-methods)
  Residual Sum of Squares and Explained Variance
• runtime.all,NMFfitXn-method
  Returns the CPU time used to perform all the NMF fits stored in
• runtime,NMFList-method
  Returns the CPU time required to compute all NMF fits in the list.
• scale.NMF
  Rescaling NMF Models
• seed(seed,ANY,ANY,character-method, seed,ANY,ANY,function-method, seed,ANY,ANY,missing-method, seed,ANY,ANY,NULL-method, seed,ANY,ANY,numeric-method, seed,ANY,list,NMFSeed-method, seed,ANY,numeric,NMFSeed-method, seed,matrix,NMF,NMFSeed-method, seed-methods)
  Interface for NMF Seeding Methods
• setNMFMethod(nmfRegisterAlgorithm)
  Registering NMF Algorithms
• setupBackend(setupLibPaths, setupRNG, setupSharedMemory, setupTempDirectory)
  Computational Setup Functions
• show,NMFfit-method
  Show method for objects of class
• show,NMFfitX1-method
  Show method for objects of class
• show,NMFfitX-method
  Show method for objects of class
• show,NMFfitXn-method
  Show method for objects of class
• show,NMFList-method
  Show method for objects of class
• show,NMF-method
  Show method for objects of class
• show,NMFns-method
  Show method for objects of class
• show,NMFOffset-method
  Show method for objects of class
• show,NMFSeed-method
  Show method for objects of class
• show,NMFStrategyIterative-method
  Show method for objects of class
• silhouette.NMF
  Silhouette of NMF Clustering
• smoothing
  Smoothing Matrix in Nonsmooth NMF Models
• sparseness(sparseness,matrix-method, sparseness-methods, sparseness,NMF-method, sparseness,numeric-method)
  Sparseness
• staticVar
  Get/Set a Static Variable in NMF Algorithms
• summary(summary-methods, summary-NMF, summary,NMFfit-method, summary,NMFfitX-method, summary,NMF-method)
  Assessing and Comparing NMF Models
• syntheticNMF
  Simulating Datasets
• t.NMF
  Transformation NMF Model Objects
• utils-NMF(str_args)
  Utility Function in the NMF Package