Man pages for NMF
Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
| advanced | Advanced Usage of the Package NMF |
| aggregate.measure | Utility function to aggregate numerical quality measures from... |
| aheatmap | Annotated Heatmaps |
| algorithm-commaNMFList-method | Returns the method names used to compute the NMF fits in the... |
| 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 |
| canFit | Testing Compatibility of Algorithm and Models |
| ccBreaks | Generate Break Intervals from Numeric Variables |
| c-commaNMF-method | Concatenating NMF Models |
| 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... |
| consensus-commaNMFfitXn-method | Computes the consensus matrix of the set of fits stored in... |
| 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... |
| 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 |
| Frobenius-nmf | NMF Algorithm/Updates for Frobenius Norm |
| gfile | Open a File Graphic Device |
| grid | Internal Grid Extension |
| heatmaps | Heatmaps of NMF Factors |
| inplace | Updating Objects In Place |
| isCRANcheck | Package Check Utils |
| KL-nmf | NMF Algorithm/Updates for Kullback-Leibler Divergence |
| latex | LaTeX Utilities for Vignettes |
| lsNMF-nmf | Multiplicative Updates for LS-NMF |
| lverbose | Internal verbosity option |
| match_atrack | Extending Annotation Vectors |
| nmf | Running NMF algorithms |
| nmfAlgorithm | Listing and Retrieving NMF Algorithms |
| nmfApply | Apply Function for NMF Objects |
| nmfCheck | Checking NMF Algorithm |
| NMF-class | Generic Interface for Nonnegative Matrix Factorisation Models |
| nmf-compare | Comparing Results from Different NMF Runs |
| NMF-defunct | Defunct Functions and Classes in the NMF Package |
| NMF-deprecated | Deprecated Functions in the Package NMF |
| nmf.equal | Testing Equality of NMF Models |
| nmfEstimateRank | Estimate Rank for NMF Models |
| NMFfit-class | Base Class for to store Nonnegative Matrix Factorisation... |
| NMFfitX | Factory Method for Multiple NMF Run Objects |
| NMFfitX1-class | Structure for Storing the Best Fit Amongst Multiple NMF Runs |
| NMFfitX-class | Virtual Class to Handle Results from Multiple Runs of NMF... |
| 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 |
| NMFns-class | NMF Model - Nonsmooth Nonnegative Matrix Factorization |
| nmfObject | Updating NMF Objects |
| NMFOffset-class | NMF Model - Nonnegative Matrix Factorization with Offset |
| NMF-package | Algorithms and framework for Nonnegative Matrix Factorization... |
| nmfReport | Run NMF Methods and Generate a Report |
| nmfSeed | Seeding Strategies for NMF Algorithms |
| NMFSeed-class | Base class that defines the interface for NMF seeding... |
| NMFstd-class | NMF Model - Standard model |
| 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... |
| nmf_update_euclidean | NMF Multiplicative Updates for Euclidean Distance |
| nmf_update_KL | NMF Multiplicative Updates for Kullback-Leibler Divergence |
| nmfWrapper | Wrapping NMF Algorithms |
| nneg | Transforming from Mixed-sign to Nonnegative Data |
| nsNMF-nmf | NMF Multiplicative Update for Nonsmooth Nonnegative Matrix... |
| objective-commaNMFfit-method | Returns the objective function associated with the algorithm... |
| offset-commaNMFfit-method | Returns the offset from the fitted model. |
| offset-commaNMFOffset-method | Offsets in NMF Models with Offset |
| 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... |
| 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 |
| RNG | Extracting RNG Data from NMF Objects |
| rnmf | Generating Random NMF Models |
| rss | Residual Sum of Squares and Explained Variance |
| runtime.all-commaNMFfitXn-method | Returns the CPU time used to perform all the NMF fits stored... |
| runtime-commaNMFList-method | Returns the CPU time required to compute all NMF fits in the... |
| 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'... |
| setup | Computational Setup Functions |
| show-commaNMFfit-method | Show method for objects of class 'NMFfit' |
| show-commaNMFfitX1-method | Show method for objects of class 'NMFfitX1' |
| show-commaNMFfitX-method | Show method for objects of class 'NMFfitX' |
| show-commaNMFfitXn-method | Show method for objects of class 'NMFfitXn' |
| show-commaNMFList-method | Show method for objects of class 'NMFList' |
| show-commaNMF-method | Show method for objects of class 'NMF' |
| show-commaNMFns-method | Show method for objects of class 'NMFns' |
| show-commaNMFOffset-method | Show method for objects of class 'NMFOffset' |
| show-commaNMFSeed-method | Show method for objects of class 'NMFSeed' |
| show-commaNMFStrategyIterative-method | Show method for objects of class 'NMFStrategyIterative' |
| silhouette.NMF | Silhouette of NMF Clustering |
| smoothing | Smoothing Matrix in Nonsmooth NMF Models |
| SNMF-nmf | NMF Algorithm - Sparse NMF via Alternating NNLS |
| sparseness | Sparseness |
| staticVar | Get/Set a Static Variable in NMF Algorithms |
| stop-NMF | Stopping Criteria for NMF Iterative Strategies |
| Strategy-class | Generic Strategy Class |
| subset-NMF | Sub-setting NMF Objects |
| syntheticNMF | Simulating Datasets |
| terms | Fixed Terms in NMF Models |
| terms-internal | Fixed Terms in NMF Models |
| t.NMF | Transformation NMF Model Objects |
| txtProgressBar | Simple Progress Bar |
| types | Testing NMF Objects |
| utils | Utility Function in the NMF Package |
