NMF: Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

Install the latest version of this package by entering the following in R:
install.packages("NMF")
AuthorRenaud Gaujoux, Cathal Seoighe
Date of publication2015-05-26 08:12:33
MaintainerRenaud Gaujoux <renaud@tx.technion.ac.il>
LicenseGPL (>= 2)
Version0.20.6
http://renozao.github.io/NMF

View on CRAN

Man pages

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...

algorithm-commaNMFStrategyOctave-method: Returns the name of the Octave/Matlab function that...

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...

NMFStrategyOctave-class: S4 Interface for Octave-Matlab NMF Algorithms

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

Functions

adata Man page
advanced-NMF Man page
aheatmap Man page
alength Man page
algorithm Man page
algorithm<- Man page
algorithmic-NMF Man page
algorithm<--methods Man page
algorithm-methods Man page
algorithm<-,NMFfit,ANY-method Man page
algorithm,NMFfit-method Man page
algorithm,NMFfitXn-method Man page
algorithm,NMFList-method Man page
algorithm<-,NMFSeed,function-method Man page
algorithm,NMFSeed-method Man page
algorithm<-,NMFStrategyFunction,function-method Man page
algorithm,NMFStrategyFunction-method Man page
algorithm<-,NMFStrategyOctave,character-method Man page
algorithm,NMFStrategyOctave-method Man page
amargin Man page
anames Man page
annotationTrack Man page
atrack Man page
.atrack Man page
.atrack,ANY-method Man page
.atrack,character-method Man page
.atrack,data.frame-method Man page
.atrack,ExpressionSet-method Man page
.atrack,matrix-method Man page
.atrack-methods Man page
basis Man page
.basis Man page
.basis<- Man page
basis<- Man page
basis,ANY-method Man page
basiscor Man page
basiscor,matrix,NMF-method Man page
basiscor-methods Man page
basiscor,NMF,matrix-method Man page
basiscor,NMF,missing-method Man page
basiscor,NMF,NMF-method Man page
basismap Man page
basismap-methods Man page
basismap,NMFfitX-method Man page
basismap,NMF-method Man page
.basis<--methods Man page
.basis-methods Man page
basis<--methods Man page
basis-methods Man page
basisnames Man page
basisnames<- Man page
basisnames<-,ANY-method Man page
basisnames,ANY-method Man page
basisnames<--methods Man page
basisnames-methods Man page
.basis<-,NMFfit,matrix-method Man page
.basis,NMFfit-method Man page
basis,NMFfitXn-method Man page
.basis<-,NMF,matrix-method Man page
.basis,NMF-method Man page
basis<-,NMF-method Man page
basis,NMF-method Man page
.basis<-,NMFstd,matrix-method Man page
.basis,NMFstd-method Man page
bioc-NMF Man page
brunet_M-nmf Man page
brunet-nmf Man page
brunet_R-nmf Man page
bterms Man page
bterms<- Man page
bterms<--methods Man page
bterms<-,NMFstd-method Man page
canFit Man page
canFit,character,ANY-method Man page
canFit-methods Man page
canFit,NMFStrategy,character-method Man page
canFit,NMFStrategy,NMF-method Man page
ccBreaks Man page
ccPalette Man page
ccRamp Man page
ccSpec Man page
checkErrors Man page
cluster_mat Man page
c,NMF-method Man page
coef Man page
.coef Man page
.coef<- Man page
coef<- Man page
coefficients Man page
coefficients-methods Man page
coefficients,NMF-method Man page
coefmap Man page
coefmap-methods Man page
coefmap,NMFfitX-method Man page
coefmap,NMF-method Man page
.coef<--methods Man page
.coef-methods Man page
coef<--methods Man page
coef-methods Man page
.coef<-,NMFfit,matrix-method Man page
.coef,NMFfit-method Man page
coef,NMFfitXn-method Man page
.coef<-,NMF,matrix-method Man page
.coef,NMF-method Man page
coef<-,NMF-method Man page
coef,NMF-method Man page
.coef<-,NMFstd,matrix-method Man page
.coef,NMFstd-method Man page
compare Man page
compare,list-method Man page
compare-methods Man page
compare-NMF Man page
compare,NMFfit-method Man page
compare,NMFfitXn-method Man page
connectivity Man page
connectivity,ANY-method Man page
connectivity,factor-method Man page
connectivity-methods Man page
connectivity,NMF-method Man page
connectivity,numeric-method Man page
consensus Man page
consensushc Man page
consensushc,matrix-method Man page
consensushc-methods Man page
consensushc,NMFfitX-method Man page
consensushc,NMF-method Man page
consensusmap Man page
consensusmap,list-method Man page
consensusmap,matrix-method Man page
consensusmap-methods Man page
consensusmap,NMFfitX-method Man page
consensusmap,NMF-method Man page
consensusmap,NMF.rank-method Man page
consensus-methods Man page
consensus,NMFfitX1-method Man page
consensus,NMFfitX-method Man page
consensus,NMFfitXn-method Man page
consensus,NMF-method Man page
cophcor Man page
cophcor,matrix-method Man page
cophcor-methods Man page
cophcor,NMFfitX-method Man page
cterms Man page
cterms<- Man page
cterms<--methods Man page
cterms<-,NMFstd-method Man page
current.vpPath_patched Man page
cutdendro Man page
deviance Man page
deviance-methods Man page
deviance,NMFfit-method Man page
deviance,NMFfitX-method Man page
deviance,NMF-method Man page
deviance,NMFStrategy-method Man page
dimnames-NMF Man page
dimnames<-,NMF-method Man page
dimnames,NMF-method Man page
dim-NMF Man page
dim,NMFfitXn-method Man page
dim,NMF-method Man page
dispersion Man page
dispersion,matrix-method Man page
dispersion-methods Man page
dispersion,NMFfitX-method Man page
.DollarNames,NMF-method Man page
entropy Man page
entropy,ANY,ANY-method Man page
entropy,factor,ANY-method Man page
entropy-methods Man page
entropy,NMFfitXn,ANY-method Man page
entropy,table,missing-method Man page
esGolub Man page
evar Man page
evar,ANY-method Man page
evar-methods Man page
existsNMFMethod Man page
existsNMFSeed Man page
extractFeatures Man page
extractFeatures,matrix-method Man page
extractFeatures-methods Man page
extractFeatures,NMF-method Man page
fcnnls Man page
.fcnnls Man page
fcnnls,ANY,numeric-method Man page
fcnnls,matrix,matrix-method Man page
fcnnls-methods Man page
fcnnls,numeric,matrix-method Man page
featureNames,NMFfitX-method Man page
featureNames<-,NMF-method Man page
featureNames,NMF-method Man page
featureScore Man page
featureScore,matrix-method Man page
featureScore-methods Man page
featureScore,NMF-method Man page
fit Man page
fit<- Man page
fit<--methods Man page
fit-methods Man page
fit,NMFfit-method Man page
fit<-,NMFfit,NMF-method Man page
fit,NMFfitX1-method Man page
fit,NMFfitX-method Man page
fit,NMFfitXn-method Man page
fitted Man page
fitted-methods Man page
fitted,NMFfit-method Man page
fitted,NMF-method Man page
fitted,NMFns-method Man page
fitted,NMFOffset-method Man page
fitted,NMFstd-method Man page
ForeachBackend Man page
ForeachBackend,ANY-method Man page
ForeachBackend,character-method Man page
ForeachBackend,cluster-method Man page
ForeachBackend,doMPI_backend-method Man page
ForeachBackend,doParallel_backend-method Man page
ForeachBackend,doParallelMC_backend-method Man page
ForeachBackend,doParallelSNOW_backend-method Man page
ForeachBackend,doPSOCK_backend-method Man page
ForeachBackend-methods Man page
ForeachBackend,missing-method Man page
ForeachBackend,mpicluster-method Man page
ForeachBackend,NULL-method Man page
ForeachBackend,numeric-method Man page
Frobenius-nmf Man page
getDoBackend Man page
getDoParHosts Man page
getDoParHosts,ANY-method Man page
getDoParHosts-methods Man page
getDoParNHosts Man page
getNMFMethod Man page
getNMFSeed Man page
.getRNG Man page
getRNG1 Man page
getRNG1-methods Man page
getRNG1,NMFfitX1-method Man page
getRNG1,NMFfitX-method Man page
getRNG1,NMFfitXn-method Man page
.getRNG-methods Man page
.getRNG,NMFfitXn-method Man page
gfile Man page
gVariable Man page
hasBasis Man page
hasCoef Man page
hasTrack Man page
heatmap-NMF Man page
hostfile Man page
ibasis Man page
ibterms Man page
ibterms-methods Man page
ibterms,NMFfit-method Man page
ibterms,NMFfitX-method Man page
ibterms,NMF-method Man page
ibterms,NMFstd-method Man page
icoef Man page
icterms Man page
icterms-methods Man page
icterms,NMFfit-method Man page
icterms,NMF-method Man page
icterms,NMFstd-method Man page
initialize,NMFOffset-method Man page
is.atrack Man page
is.empty.nmf Man page
is.mixed Man page
is.nmf Man page
isNMFfit Man page
is.partial.nmf Man page
iterms Man page
KL-nmf Man page
lee-nmf Man page
lee_R-nmf Man page
loadings,NMF-method Man page
logs Man page
logs,ANY-method Man page
logs-methods Man page
lsNMF-nmf Man page
lverbose Man page
match_atrack Man page
metagenes Man page
metagenes<- Man page
metaHeatmap Man page
metaHeatmap,matrix-method Man page
metaHeatmap-methods Man page
metaHeatmap,NMFfitX-method Man page
metaHeatmap,NMF-method Man page
metaprofiles Man page
metaprofiles<- Man page
methods-NMF Man page
minfit Man page
minfit-methods Man page
minfit,NMFfit-method Man page
minfit,NMFfitX1-method Man page
minfit,NMFfitX-method Man page
minfit,NMFfitXn-method Man page
misc Man page
modelname Man page
modelname,ANY-method Man page
modelname-methods Man page
modelname,NMFfit-method Man page
modelname,NMFfitXn-method Man page
modelname,NMFStrategy-method Man page
name Man page
name<- Man page
name<--methods Man page
name-methods Man page
name<-,Strategy,character-method Man page
name,Strategy-method Man page
nbasis Man page
nbasis,ANY-method Man page
nbasis-methods Man page
nbasis,NMFfitXn-method Man page
nbterms Man page
ncterms Man page
neq.constraints.inplace Man page
niter Man page
niter<- Man page
niter<--methods Man page
niter-methods Man page
niter,NMFfit-method Man page
niter<-,NMFfit,numeric-method Man page
nmeta Man page
nmf Man page
NMF Man page
nmfAlgorithm Man page
nmfAlgorithm.brunet Man page
nmfAlgorithm.brunet_M Man page
nmfAlgorithm.brunet_R Man page
nmfAlgorithm.Frobenius Man page
nmfAlgorithm.KL Man page
nmfAlgorithm.lee Man page
nmfAlgorithm.lee_R Man page
nmfAlgorithm.lsNMF Man page
nmfAlgorithm.nsNMF Man page
nmfAlgorithm.nsNMF_R Man page
nmfAlgorithm.offset Man page
nmfAlgorithm.offset_R Man page
nmfAlgorithm.SNMF_L Man page
nmfAlgorithm.SNMF_R Man page
nmfApply Man page
nmfArgs Man page
nmfCheck Man page
NMF-class Man page
nmf,data.frame,ANY,ANY-method Man page
NMF-defunct Man page
NMF-deprecated Man page
nmfDistance Man page
nmf.equal Man page
nmf.equal,list,list-method Man page
nmf.equal,list,missing-method Man page
nmf.equal-methods Man page
nmf.equal,NMFfit,NMFfit-method Man page
nmf.equal,NMFfit,NMF-method Man page
nmf.equal,NMFfitX1,NMFfitX1-method Man page
nmf.equal,NMFfitX,NMF-method Man page
nmf.equal,NMF,NMFfit-method Man page
nmf.equal,NMF,NMFfitX-method Man page
nmf.equal,NMF,NMF-method Man page
nmfEstimateRank Man page
nmf,ExpressionSet,ANY,ANY-method Man page
NMFfit Man page
NMFfit-class Man page
NMFfitX Man page
NMFfitX1-class Man page
NMFfitX-class Man page
NMFfitX,list-method Man page
NMFfitX-methods Man page
NMFfitXn-class Man page
NMFfitX,NMFfit-method Man page
NMFfitX,NMFfitX-method Man page
nmfFormals Man page
nmf,formula,ANY,ANY-method Man page
nmf.getOption Man page
NMFList-class Man page
nmf,matrix,data.frame,ANY-method Man page
nmf,matrix,ExpressionSet,ANY-method Man page
nmf,matrix,matrix,ANY-method Man page
nmf,matrix,missing,ANY-method Man page
nmf,matrix,NMF,ANY-method Man page
nmf,matrix,NULL,ANY-method Man page
nmf,matrix,numeric,character-method Man page
nmf,matrix,numeric,function-method Man page
nmf,matrix,numeric,list-method Man page
nmf,matrix,numeric,missing-method Man page
nmf,matrix,numeric,NMFStrategy-method Man page
nmf,matrix,numeric,NULL-method Man page
[,NMF-method Man page
$<-,NMF-method Man page
$,NMF-method Man page
nmf-methods Man page
nmfModel Man page
nmfModel,ANY,ExpressionSet-method Man page
nmfModel,data.frame,data.frame-method Man page
nmfModel,ExpressionSet,ANY-method Man page
nmfModel,formula,ANY-method Man page
nmfModel,matrix,ANY-method Man page
nmfModel,matrix,matrix-method Man page
nmfModel-methods Man page
nmfModel,missing,ANY-method Man page
nmfModel,missing,missing-method Man page
nmfModel,NULL,ANY-method Man page
nmfModel,numeric,matrix-method Man page
nmfModel,numeric,missing-method Man page
nmfModel,numeric,numeric-method Man page
nmfModels Man page
NMFns-class Man page
nmfObject Man page
NMFOffset-class Man page
nmf.options Man page
NMF-package Man page
nmf.printOptions Man page
nmfRegisterAlgorithm Man page
nmfReport Man page
nmf.resetOptions Man page
nmfSeed Man page
NMFSeed Man page
NMFSeed,character-method Man page
NMFSeed-class Man page
NMFSeed-methods Man page
NMFSeed,NMFSeed-method Man page
NMFstd-class Man page
NMFStop Man page
nmf.stop.connectivity Man page
nmf.stop.iteration Man page
nmf.stop.stationary Man page
nmf.stop.threshold Man page
NMFStrategy Man page
NMFStrategy,character,character-method Man page
NMFStrategy,character,function-method Man page
NMFStrategy,character,missing-method Man page
NMFStrategy,character,NMFStrategy-method Man page
NMFStrategy-class Man page
NMFStrategyFunction-class Man page
NMFStrategyIterative-class Man page
NMFStrategy-methods Man page
NMFStrategy,missing,character-method Man page
NMFStrategy,NMFStrategy,missing-method Man page
NMFStrategy,NULL,character-method Man page
NMFStrategy,NULL,NMFStrategy-method Man page
NMFStrategyOctave-class Man page
nmf_update.brunet Man page
nmf_update.brunet_R Man page
nmf_update.euclidean Man page
nmf_update.euclidean.h Man page
nmf_update.euclidean.h_R Man page
nmf_update.euclidean_offset.h Man page
nmf_update.euclidean_offset.w Man page
nmf_update.euclidean.w Man page
nmf_update.euclidean.w_R Man page
nmf_update.KL Man page
nmf_update.KL.h Man page
nmf_update.KL.h_R Man page
nmf_update.KL.w Man page
nmf_update.KL.w_R Man page
nmf_update.lee Man page
nmf_update.lee_R Man page
nmf_update.lsnmf Man page
nmf_update.ns Man page
nmf_update.ns_R Man page
nmf_update.offset Man page
nmf_update.offset_R Man page
nmfWrapper Man page
nneg Man page
nneg,ExpressionSet-method Man page
nneg,matrix-method Man page
nneg-methods Man page
nneg,NMF-method Man page
nrun Man page
nrun,ANY-method Man page
nrun-methods Man page
nrun,NMFfit-method Man page
nrun,NMFfitX1-method Man page
nrun,NMFfitX-method Man page
nrun,NMFfitXn-method Man page
nsNMF_R-nmf Man page
nterms Man page
objective Man page
objective<- Man page
objective<--methods Man page
objective-methods Man page
objective<-,NMFfit,ANY-method Man page
objective,NMFfit-method Man page
objective<-,NMFStrategy,character-method Man page
objective<-,NMFStrategy,function-method Man page
objective,NMFStrategy-method Man page
offset,NMFfit-method Man page
offset,NMFOffset-method Man page
offset_R-nmf Man page
options-NMF Man page
parallel-NMF Man page
parse_formula Man page
plot.NMF.consensus Man page
plot,NMFfit,missing-method Man page
plot,NMFList,missing-method Man page
plot.NMF.rank Man page
pmax.inplace Man page
posneg Man page
predict Man page
predict-methods Man page
predict,NMFfitX-method Man page
predict,NMF-method Man page
profcor Man page
profcor,matrix,NMF-method Man page
profcor-methods Man page
profcor,NMF,matrix-method Man page
profcor,NMF,missing-method Man page
profcor,NMF,NMF-method Man page
profplot Man page
profplot.default Man page
purity Man page
purity,ANY,ANY-method Man page
purity,factor,ANY-method Man page
purity-methods Man page
purity,NMFfitXn,ANY-method Man page
purity,table,missing-method Man page
randomize Man page
register Man page
registerDoBackend Man page
removeNMFMethod Man page
removeNMFSeed Man page
residuals Man page
residuals<- Man page
residuals<--methods Man page
residuals-methods Man page
residuals<-,NMFfit-method Man page
residuals,NMFfit-method Man page
residuals,NMFfitX-method Man page
revPalette Man page
rmatrix Man page
rmatrix,ANY-method Man page
rmatrix-methods Man page
rmatrix,NMF-method Man page
rmatrix,numeric-method Man page
rnmf Man page
rnmf,ANY,data.frame-method Man page
rnmf,ANY,ExpressionSet-method Man page
rnmf,ANY,matrix-method Man page
rnmf,formula,ANY-method Man page
rnmf-methods Man page
rnmf,missing,missing-method Man page
rnmf,NMF,missing-method Man page
rnmf,NMF,numeric-method Man page
rnmf,NMFOffset,numeric-method Man page
rnmf,numeric,missing-method Man page
rnmf,numeric,numeric-method Man page
rposneg Man page
rposneg,ExpressionSet-method Man page
rposneg,matrix-method Man page
rposneg-methods Man page
rposneg,NMF-method Man page
rss Man page
rss,ANY-method Man page
rss,matrix-method Man page
rss-methods Man page
run Man page
run-methods Man page
run,NMFStrategy,ExpressionSet,ANY-method Man page
run,NMFStrategyFunction,matrix,NMFfit-method Man page
run,NMFStrategyIterative,matrix,NMFfit-method Man page
run,NMFStrategyIterativeX,matrix,NMFfit-method Man page
run,NMFStrategy,matrix,NMFfit-method Man page
run,NMFStrategy,matrix,NMF-method Man page
run,NMFStrategyOctave,matrix,NMFfit-method Man page
runtime Man page
runtime.all Man page
runtime.all-methods Man page
runtime.all,NMFfit-method Man page
runtime.all,NMFfitX-method Man page
runtime.all,NMFfitXn-method Man page
runtime-methods Man page
runtime,NMFfit-method Man page
runtime,NMFList-method Man page
sampleNames<-,NMF,ANY-method Man page
sampleNames,NMFfitX-method Man page
sampleNames,NMF-method Man page
scale.NMF Man page
scoef Man page
scoef,matrix-method Man page
scoef-methods Man page
scoef,NMF-method Man page
seed Man page
seed,ANY,ANY,character-method Man page
seed,ANY,ANY,function-method Man page
seed,ANY,ANY,missing-method Man page
seed,ANY,ANY,NULL-method Man page
seed,ANY,ANY,numeric-method Man page
seed,ANY,list,NMFSeed-method Man page
seed,ANY,numeric,NMFSeed-method Man page
seed,ExpressionSet,ANY,ANY-method Man page
seeding Man page
seeding<- Man page
seeding<--methods Man page
seeding-methods Man page
seeding<-,NMFfit-method Man page
seeding,NMFfit-method Man page
seeding,NMFfitXn-method Man page
seed,matrix,NMF,NMFSeed-method Man page
seed-methods Man page
selectNMFMethod Man page
seqtime Man page
seqtime-methods Man page
seqtime,NMFfitXn-method Man page
seqtime,NMFList-method Man page
setDoBackend Man page
setNMFMethod Man page
setNMFSeed Man page
setupBackend Man page
setupLibPaths Man page
setupRNG Man page
setupSharedMemory Man page
setupTempDirectory Man page
show,NMFfit-method Man page
show,NMFfitX1-method Man page
show,NMFfitX-method Man page
show,NMFfitXn-method Man page
show,NMFList-method Man page
show,NMF-method Man page
show,NMFns-method Man page
show,NMFOffset-method Man page
show,NMFSeed-method Man page
show,NMFStrategyIterative-method Man page
show,NMFStrategy-method Man page
show,NMFStrategyOctave-method Man page
silhouette.NMF Man page
smoothing Man page
SNMF/L-nmf Man page
SNMF/R-nmf Man page
sparseness Man page
sparseness,matrix-method Man page
sparseness-methods Man page
sparseness,NMF-method Man page
sparseness,numeric-method Man page
staticVar Man page
stop-NMF Man page
str_args Man page
Strategy-class Man page
summary Man page
summary-methods Man page
summary-NMF Man page
summary,NMFfit-method Man page
summary,NMFfitX-method Man page
summary,NMFList-method Man page
summary,NMF-method Man page
syntheticNMF Man page
t.NMF Man page
trackError Man page
tryViewport Man page
ts_eval Man page
ts_tempfile Man page
txtProgressBar Man page
.use.grid.patch Man page
utils-NMF Man page
which.best Man page
wrss Man page

Files

TODO
inst
inst/CITATION
inst/REFERENCES.bib
inst/tests
inst/tests/runit.NMFfit-class.r inst/tests/runit.interface.r inst/tests/runit.aheatmap.R inst/tests/runit.NMFSet.r inst/tests/runit.bioc.r inst/tests/runit.NMFclass.r inst/tests/runit.distance.r inst/tests/runit.utils.r inst/tests/runit.NMFStrategy-class.r inst/tests/runit.parallel.r inst/tests/runit.options.r inst/tests/runit.algorithms.r inst/tests/runit.seed.r
inst/scripts
inst/scripts/report.Rmd
inst/scripts/grid.R
inst/doc
inst/doc/heatmaps.Rnw
inst/doc/NMF-unitTests.Rnw
inst/doc/NMF-vignette.R inst/doc/NMF-unitTests.R
inst/doc/NMF-unitTests.pdf
inst/doc/consensus.pdf
inst/doc/NMF-vignette.pdf
inst/doc/heatmaps.pdf
inst/doc/NMF-vignette.Rnw
inst/doc/heatmaps.R
inst/m-files
inst/m-files/brunet.R
inst/m-files/brunet-run.m
inst/m-files/brunet.m
tests
tests/doRUnit.R
src
src/divergence.cpp
src/euclidean.cpp
src/utils.cpp
src/distance.cpp
NAMESPACE
demo
demo/aheatmap.R
demo/00Index
demo/nmf.R demo/heatmaps.R
NEWS
data
data/esGolub.rda
R
R/extractFeatures.R R/Bioc-layer.R R/utils.R R/NMFStrategy-class.R R/atracks.R R/registry.R R/algorithms-brunet.R R/parallel.R R/seed-base.R R/versions.R R/NMFSet-class.R R/NMFOffset-class.R R/nmfModel.R R/registry-seed.R R/NMFstd-class.R R/NMFns-class.R R/aheatmap.R R/NMFStrategyIterative-class.R R/NMFplots.R R/data.R R/simulation.R R/seed-ica.R R/setNMFClass.R R/algorithms-base.R R/options.R R/NMF-class.R R/NMFStrategyFunction-class.R R/colorcode.R R/algorithms-lnmf.R R/run.R R/NMFSeed-class.R R/algorithms-snmf.R R/NMFStrategyOctave-class.R R/nmf.R R/registry-algorithms.R R/seed-nndsvd.R R/rmatrix.R R/algorithmic.R R/rnmf.R R/nmf-package.R R/grid.R R/fixed-terms.R R/transforms.R R/NMFfit-class.R R/algorithms-pe-nmf.R R/algorithms-siNMF.R R/algorithms-lsnmf.R R/heatmaps.R R/tests.R
vignettes
vignettes/heatmaps.Rnw
vignettes/NMF-unitTests.Rnw
vignettes/src
vignettes/src/bmc.R
vignettes/consensus.pdf
vignettes/.install_extras
vignettes/NMF-vignette.Rnw
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/smoothing.Rd man/offset-nmf.Rd man/txtProgressBar.Rd man/setNMFSeed.Rd man/silhouette.NMF.Rd man/cophcor.Rd man/consensus-commaNMFfitX1-method.Rd man/NMFfitX-class.Rd man/fit.Rd man/bioc.Rd man/NMF-package.Rd man/staticVar.Rd man/seed.Rd man/show-commaNMFStrategyIterative-method.Rd man/advanced.Rd man/nmf.Rd man/types.Rd man/setNMFMethod.Rd man/NMFList-class.Rd man/nmf.equal.Rd man/terms-internal.Rd man/lsNMF-nmf.Rd man/deviance.Rd man/offset-commaNMFOffset-method.Rd man/residuals.Rd man/NMFfitXn-class.Rd man/NMFstd-class.Rd man/checkErrors.Rd man/nmfWrapper.Rd man/nmfModel.Rd man/scores.Rd man/nsNMF-nmf.Rd man/show-commaNMFfitX-method.Rd man/show-commaNMFfitXn-method.Rd man/parse_formula.Rd man/algorithm-commaNMFList-method.Rd man/nmfApply.Rd man/ccBreaks.Rd man/show-commaNMFfit-method.Rd man/nmfObject.Rd man/profplot.Rd man/NMFSeed-class.Rd man/runtime.all-commaNMFfitXn-method.Rd man/nmfEstimateRank.Rd man/basiscor.Rd man/subset-NMF.Rd man/revPalette.Rd man/rss.Rd man/show-commaNMFOffset-method.Rd man/connectivity.Rd man/rmatrix.Rd man/parallel.Rd man/plot-commaNMFfit-commamissing-method.Rd man/Strategy-class.Rd man/ccPalette.Rd man/offset-commaNMFfit-method.Rd man/nmf_update_KL.Rd man/nmfCheck.Rd man/aheatmap.Rd man/utils.Rd man/rnmf.Rd man/assess.Rd man/cutdendro.Rd man/predict.Rd man/randomize.Rd man/algorithm-commaNMFStrategyOctave-method.Rd man/NMFStrategyIterative-class.Rd man/NMF-defunct.Rd man/nmf_update_euclidean.Rd man/options.Rd man/nneg.Rd man/ccSpec.Rd man/NMF-class.Rd man/SNMF-nmf.Rd man/cluster_mat.Rd man/NMFStrategy-class.Rd man/sparseness.Rd man/KL-nmf.Rd man/c-commaNMF-method.Rd man/basis-coef-methods.Rd man/NMFns-class.Rd man/NMF-deprecated.Rd man/consensus-commaNMFfitXn-method.Rd man/nmfFormals.Rd man/lverbose.Rd man/fcnnls.Rd man/NMFStrategyFunction-class.Rd man/purity.Rd man/nmf-compare.Rd man/NMFOffset-class.Rd man/heatmaps.Rd man/NMFStrategyOctave-class.Rd man/dims.Rd man/nmfReport.Rd man/stop-NMF.Rd man/inplace.Rd man/algorithmic.Rd man/runtime-commaNMFList-method.Rd man/show-commaNMFns-method.Rd man/scale.NMF.Rd man/atrack.Rd man/grid.Rd man/foreach.Rd man/fitted.Rd man/gfile.Rd man/canFit.Rd man/ccRamp.Rd man/terms.Rd man/dispersion.Rd man/consensushc.Rd man/match_atrack.Rd man/show-commaNMFfitX1-method.Rd man/dimnames.Rd man/registry-algorithm.Rd man/NMFfit-class.Rd man/show-commaNMFSeed-method.Rd man/setup.Rd man/show-commaNMF-method.Rd man/syntheticNMF.Rd man/nmfSeed.Rd man/objective-commaNMFfit-method.Rd man/show-commaNMFList-method.Rd man/NMFfitX.Rd man/dot-fcnnls.Rd man/NMFfitX1-class.Rd man/RNG.Rd man/NMFStrategy.Rd man/Frobenius-nmf.Rd man/esGolub.Rd man/t.NMF.Rd man/nmfAlgorithm.Rd
.Rinstignore

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.