Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

advanced | Advanced Usage of the Package NMF |

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 |

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

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 |

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