Algorithms and framework for Nonnegative Matrix Factorization (NMF).


[Up] [Top]

Documentation for package ‘NMF’ version 0.4

Help Pages

A B C D E F I M N O P R S misc

-- --

NMF-package NMF Package Overview

-- --

$ Base Class for to store Nonnegative Matrix Factorisation results
$-method Base Class for to store Nonnegative Matrix Factorisation results
$<- Base Class for to store Nonnegative Matrix Factorisation results
$<--method Base Class for to store Nonnegative Matrix Factorisation results

-- A --

algorithm Base Class for to store Nonnegative Matrix Factorisation results
algorithm-method Class "NMFList" to Handle the Comparison of NMF Results
algorithm-method Base Class for to store Nonnegative Matrix Factorisation results
algorithm-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
algorithm<- Base Class for to store Nonnegative Matrix Factorisation results
algorithm<--method Base Class for to store Nonnegative Matrix Factorisation results
as.NMFList Comparing Results from Different NMF Runs
as.NMFList-method Comparing Results from Different NMF Runs
as.NMFList-methods Comparing Results from Different NMF Runs

-- B --

basis Extract/Set the matrix of basis vectors from a NMF model
basis-method Base Class for to store Nonnegative Matrix Factorisation results
basis-method Implement of the standard NMF model
basis-method Extract/Set the matrix of basis vectors from a NMF model
basis-methods Extract/Set the matrix of basis vectors from a NMF model
basis<- Extract/Set the matrix of basis vectors from a NMF model
basis<--method Base Class for to store Nonnegative Matrix Factorisation results
basis<--method Implement of the standard NMF model
basis<--method Extract/Set the matrix of basis vectors from a NMF model
basis<--methods Extract/Set the matrix of basis vectors from a NMF model

-- C --

coef Extract/Set the matrix of basis vectors from a NMF model
coef-method Base Class for to store Nonnegative Matrix Factorisation results
coef-method Implement of the standard NMF model
coef-method Extract/Set the matrix of basis vectors from a NMF model
coef<- Extract/Set the matrix of basis vectors from a NMF model
coef<--method Base Class for to store Nonnegative Matrix Factorisation results
coef<--method Implement of the standard NMF model
coef<--method Extract/Set the matrix of basis vectors from a NMF model
coef<--methods Extract/Set the matrix of basis vectors from a NMF model
coefficients Extract/Set the matrix of basis vectors from a NMF model
coefficients-method Extract/Set the matrix of basis vectors from a NMF model
coefficients<--method Extract/Set the matrix of basis vectors from a NMF model
compare Comparing Results from Different NMF Runs
compare-method Comparing Results from Different NMF Runs
compare-methods Comparing Results from Different NMF Runs
connectivity Class and Utility Methods for NMF objects
connectivity-method Class and Utility Methods for NMF objects
connectivity-methods Class and Utility Methods for NMF objects
consensus Handling Results from Multiple NMF Runs
consensus-method Interface Class for Nonnegative Matrix Factorisation Models
consensus-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
consensus-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
consensus-methods Handling Results from Multiple NMF Runs
cophcor Handling Results from Multiple NMF Runs
cophcor-method Handling Results from Multiple NMF Runs
cophcor-methods Handling Results from Multiple NMF Runs

-- D --

dim-method Interface Class for Nonnegative Matrix Factorisation Models
dim-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
dimnames-method Interface Class for Nonnegative Matrix Factorisation Models
dimnames<--method Interface Class for Nonnegative Matrix Factorisation Models
dispersion Handling Results from Multiple NMF Runs
dispersion-method Handling Results from Multiple NMF Runs
dispersion-methods Handling Results from Multiple NMF Runs
distance Interface Class for Nonnegative Matrix Factorisation Models
distance-method Layer to use the NMF package within Bioconductor
distance-method Interface Class for Nonnegative Matrix Factorisation Models
distance-method Base Class for to store Nonnegative Matrix Factorisation results

-- E --

entropy Class and Utility Methods for NMF objects
entropy-method Class and Utility Methods for NMF objects
entropy-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
entropy-methods Class and Utility Methods for NMF objects
esGolub Golub ExpressionSet from Brunet et al. Paper
evar Class and Utility Methods for NMF objects
evar-method Class and Utility Methods for NMF objects
evar-methods Class and Utility Methods for NMF objects
extractFeatures Class and Utility Methods for NMF objects
extractFeatures-method Class and Utility Methods for NMF objects

-- F --

featureNames Interface Class for Nonnegative Matrix Factorisation Models
featureNames-method Interface Class for Nonnegative Matrix Factorisation Models
featureNames-method Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
featureNames<- Interface Class for Nonnegative Matrix Factorisation Models
featureNames<--method Interface Class for Nonnegative Matrix Factorisation Models
featureScore Class and Utility Methods for NMF objects
featureScore-method Class and Utility Methods for NMF objects
fit Base Class for to store Nonnegative Matrix Factorisation results
fit-method Base Class for to store Nonnegative Matrix Factorisation results
fit-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
fit-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
fit-method Handling Results from Multiple NMF Runs
fit-methods Base Class for to store Nonnegative Matrix Factorisation results
fit<- Base Class for to store Nonnegative Matrix Factorisation results
fit<--method Base Class for to store Nonnegative Matrix Factorisation results
fitted-method Interface Class for Nonnegative Matrix Factorisation Models
fitted-method Nonnegative Matrix Factorization with Offset
fitted-method Base Class for to store Nonnegative Matrix Factorisation results
fitted-method Nonsmooth Nonnegative Matrix Factorization
fitted-method Implement of the standard NMF model

-- I --

initialize-method Nonnegative Matrix Factorization with Offset
is.empty.nmf Interface Class for Nonnegative Matrix Factorisation Models
is.empty.nmf-method Interface Class for Nonnegative Matrix Factorisation Models

-- M --

metagenes Layer to use the NMF package within Bioconductor
metagenes-method Layer to use the NMF package within Bioconductor
metagenes-methods Layer to use the NMF package within Bioconductor
metagenes<- Layer to use the NMF package within Bioconductor
metagenes<--method Layer to use the NMF package within Bioconductor
metaHeatmap Class and Utility Methods for NMF objects
metaHeatmap-method Class and Utility Methods for NMF objects
metaHeatmap-method Handling Results from Multiple NMF Runs
metaHeatmap-methods Class and Utility Methods for NMF objects
metaprofiles Layer to use the NMF package within Bioconductor
metaprofiles-method Layer to use the NMF package within Bioconductor
metaprofiles-methods Layer to use the NMF package within Bioconductor
metaprofiles<- Layer to use the NMF package within Bioconductor
metaprofiles<--method Layer to use the NMF package within Bioconductor
modelname Interface Class for Nonnegative Matrix Factorisation Models
modelname-method Interface Class for Nonnegative Matrix Factorisation Models
modelname-method Base Class for to store Nonnegative Matrix Factorisation results

-- N --

nbasis Interface Class for Nonnegative Matrix Factorisation Models
nbasis-method Interface Class for Nonnegative Matrix Factorisation Models
nmeta Layer to use the NMF package within Bioconductor
nmeta-method Layer to use the NMF package within Bioconductor
nmeta-methods Layer to use the NMF package within Bioconductor
NMF NMF Package Overview
nmf Main Interface to run NMF algorithms
NMF Algorithms Main Interface to run NMF algorithms
NMF-advanced Advanced usage of package NMF
NMF-bioc Layer to use the NMF package within Bioconductor
NMF-class Interface Class for Nonnegative Matrix Factorisation Models
nmf-compare Comparing Results from Different NMF Runs
nmf-method Main Interface to run NMF algorithms
nmf-methods Main Interface to run NMF algorithms
nmf-multiple Handling Results from Multiple NMF Runs
NMF-utils Class and Utility Methods for NMF objects
nmf.getOption Advanced usage of package NMF
nmf.options Advanced usage of package NMF
nmf.options.reset Advanced usage of package NMF
nmf.options.runtime Advanced usage of package NMF
nmfApply Class and Utility Methods for NMF objects
nmfApply-method Class and Utility Methods for NMF objects
nmfEstimateRank Estimate optimal rank for Nonnegative Matrix Factorization (NMF) models
NMFfit-class Base Class for to store Nonnegative Matrix Factorisation results
NMFfitX-class Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
NMFfitX1-class Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
NMFfitXn-class Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
NMFList-class Class "NMFList" to Handle the Comparison of NMF Results
nmfModel Factory Method for NMF Models
nmfModel-method Factory Method for NMF Models
nmfModel-methods Factory Method for NMF Models
NMFns-class Nonsmooth Nonnegative Matrix Factorization
NMFOffset-class Nonnegative Matrix Factorization with Offset
NMFSet-class Deprecated Class to store results from multiple runs of NMF algorithms
NMFstd-class Implement of the standard NMF model
nrun Handling Results from Multiple NMF Runs
nrun-method Base Class for to store Nonnegative Matrix Factorisation results
nrun-method Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
nrun-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
nrun-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
nrun-methods Handling Results from Multiple NMF Runs

-- O --

objective Base Class for to store Nonnegative Matrix Factorisation results
objective-method Base Class for to store Nonnegative Matrix Factorisation results
objective<- Base Class for to store Nonnegative Matrix Factorisation results
objective<--method Base Class for to store Nonnegative Matrix Factorisation results
offset-method Nonnegative Matrix Factorization with Offset

-- P --

plot-method Class and Utility Methods for NMF objects
plot-method Comparing Results from Different NMF Runs
plot.NMF.rank Estimate optimal rank for Nonnegative Matrix Factorization (NMF) models
predict Class and Utility Methods for NMF objects
predict-method Class and Utility Methods for NMF objects
predict-method Handling Results from Multiple NMF Runs
predict-methods Class and Utility Methods for NMF objects
purity Class and Utility Methods for NMF objects
purity-method Class and Utility Methods for NMF objects
purity-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
purity-methods Class and Utility Methods for NMF objects

-- R --

randomize Class and Utility Methods for NMF objects
residuals Class and Utility Methods for NMF objects
residuals-method Class and Utility Methods for NMF objects
residuals-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
residuals<- Base Class for to store Nonnegative Matrix Factorisation results
residuals<--method Base Class for to store Nonnegative Matrix Factorisation results
residuals<--methods Base Class for to store Nonnegative Matrix Factorisation results
rnmf Interface Class for Nonnegative Matrix Factorisation Models
rnmf-method Interface Class for Nonnegative Matrix Factorisation Models
rnmf-method Nonnegative Matrix Factorization with Offset
rnmf-methods Interface Class for Nonnegative Matrix Factorisation Models
rss Class and Utility Methods for NMF objects
rss-method Class and Utility Methods for NMF objects
runtime Base Class for to store Nonnegative Matrix Factorisation results
runtime-method Class "NMFList" to Handle the Comparison of NMF Results
runtime-method Base Class for to store Nonnegative Matrix Factorisation results
runtime.all Handling Results from Multiple NMF Runs
runtime.all-method Base Class for to store Nonnegative Matrix Factorisation results
runtime.all-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
runtime.all-method Handling Results from Multiple NMF Runs
runtime.all-methods Handling Results from Multiple NMF Runs

-- S --

sampleNames Interface Class for Nonnegative Matrix Factorisation Models
sampleNames-method Interface Class for Nonnegative Matrix Factorisation Models
sampleNames-method Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
sampleNames<- Interface Class for Nonnegative Matrix Factorisation Models
sampleNames<--method Interface Class for Nonnegative Matrix Factorisation Models
seed Main Interface to run NMF algorithms
seeding Base Class for to store Nonnegative Matrix Factorisation results
seeding-method Base Class for to store Nonnegative Matrix Factorisation results
seeding-methods Base Class for to store Nonnegative Matrix Factorisation results
seeding<- Base Class for to store Nonnegative Matrix Factorisation results
seeding<--method Base Class for to store Nonnegative Matrix Factorisation results
seqtime Handling Results from Multiple NMF Runs
seqtime-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
seqtime-methods Handling Results from Multiple NMF Runs
show-method Interface Class for Nonnegative Matrix Factorisation Models
show-method Class "NMFList" to Handle the Comparison of NMF Results
show-method Nonnegative Matrix Factorization with Offset
show-method Base Class for to store Nonnegative Matrix Factorisation results
show-method Virtual Class to Handle Results from Multiple Runs of a NMF Algorithms
show-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Only the Best Fit is Kept
show-method Class to Store the Result from Multiple Runs of a NMF Algorithm when Keeping All the Fits
show-method Nonsmooth Nonnegative Matrix Factorization
smoothing Nonsmooth Nonnegative Matrix Factorization
smoothing-method Nonsmooth Nonnegative Matrix Factorization
smoothing-methods Nonsmooth Nonnegative Matrix Factorization
sparseness Class and Utility Methods for NMF objects
sparseness-method Class and Utility Methods for NMF objects
sparseness-methods Class and Utility Methods for NMF objects
summary-method Interface Class for Nonnegative Matrix Factorisation Models
summary-method Base Class for to store Nonnegative Matrix Factorisation results
summary-method Comparing Results from Different NMF Runs
summary-method Handling Results from Multiple NMF Runs
syntheticNMF Class and Utility Methods for NMF objects

-- misc --

[-method Interface Class for Nonnegative Matrix Factorisation Models