Containers and tools for dimensionally-reduced -omics representations

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Documentation for package ‘ReducedExperiment’ version 0.99.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.DollarNames.FactorisedExperiment	Command line completion for '$'
.DollarNames.ModularExperiment	Command line completion for '$'
.DollarNames.ReducedExperiment	Command line completion for '$'
.FactorisedExperiment	FactorisedExperiment: A container for the results of factor analysis
.ModularExperiment	ModularExperiment: A container for the results of module analysis
.ReducedExperiment	ReducedExperiment: A container for dimensionally-reduced representations
assessSoftThreshold	Assess soft thresholding power for WGCNA
assignments	Get and set module feature assignments
assignments-method	Get and set module feature assignments
assignments<-	Get and set module feature assignments
assignments<--method	Get and set module feature assignments
associateComponents	Runs linear models for components and sample-level data
calcEigengenes	Calculate eigengenes for new data
calcEigengenes-method	Calculate eigengenes for new data
cbind-method	Combine ReducedExperiment objects by columns or rows
cbind_rbind	Combine ReducedExperiment objects by columns or rows
colnames<--method	Get sample names
componentNames	Get names of dimensionally-reduced components
componentNames-method	Get names of dimensionally-reduced components
componentNames<-	Get names of dimensionally-reduced components
componentNames<--method	Get names of dimensionally-reduced components
dendrogram	Get the dendrogram stored in a ModularExperiment
dendrogram-method	Get the dendrogram stored in a ModularExperiment
dendrogram<-	Get the dendrogram stored in a ModularExperiment
dendrogram<--method	Get the dendrogram stored in a ModularExperiment
dim-method	Get the dimensions of a Reducedexperiment object
dollar_names	Command line completion for '$'
estimateFactors	Perform dimensionality reduction using Independent Component Analysis
estimateStability	Estimate stability of factors as a function of the number of components
FactorisedExperiment	FactorisedExperiment: A container for the results of factor analysis
FactorisedExperiment-class	FactorisedExperiment: A container for the results of factor analysis
featureNames	Get feature names
featureNames-method	Get feature names
featureNames<-	Get feature names
featureNames<--method	Get feature names
getAlignedFeatures	Get feature alignments with factors
getAlignedFeatures-method	Get feature alignments with factors
getCentrality	Get correlation of features with module eigengenes
getCentrality-method	Get correlation of features with module eigengenes
getCommonFeatures	Get common factor features
getGeneIDs	Gets alternative gene annotations from biomaRt
getGeneIDs-method	Gets alternative gene annotations from biomaRt
getMsigdbT2G	Get TERM2GENE dataframe from MSigDB
identifyModules	Apply dimensionality reduction using Weighted Gene Correlation Network Analysis
individual_dim	Prints individual lengths of samples, components and features
loadings	Get and set loadings
loadings-method	Get and set loadings
loadings<-	Get and set loadings
loadings<--method	Get and set loadings
ModularExperiment	ModularExperiment: A container for the results of module analysis
ModularExperiment-class	ModularExperiment: A container for the results of module analysis
moduleNames	Get names of dimensionally-reduced components
moduleNames-method	Get names of dimensionally-reduced components
moduleNames<-	Get names of dimensionally-reduced components
moduleNames<--method	Get names of dimensionally-reduced components
modulePreservation	Get module preservation statistics
names<--method	Get feature names
nComponents	Prints individual lengths of samples, components and features
nComponents-method	Prints individual lengths of samples, components and features
nFeatures	Prints individual lengths of samples, components and features
nFeatures-method	Prints individual lengths of samples, components and features
nModules	Prints individual lengths of samples, components and features
nModules-method	Prints individual lengths of samples, components and features
nSamples	Prints individual lengths of samples, components and features
nSamples-method	Prints individual lengths of samples, components and features
plotCommonFeatures	Heatmap comparing commonality across factors
plotDendro	Plot a dendrogram stored in a ModularExperiment
plotDendro-method	Plot a dendrogram stored in a ModularExperiment
plotModulePreservation	Plot module preservation statistics
plotStability	Plot component stability as a function of the number of components
predict-method	Calculate eigengenes for new data
predict-method	Project new data using pre-defined factors
projectData	Project new data using pre-defined factors
projectData-method	Project new data using pre-defined factors
rbind-method	Combine ReducedExperiment objects by columns or rows
reduced	Get and set reduced data
reduced-method	Get and set reduced data
reduced<-	Get and set reduced data
reduced<--method	Get and set reduced data
ReducedExperiment	ReducedExperiment: A container for dimensionally-reduced representations
ReducedExperiment-class	ReducedExperiment: A container for dimensionally-reduced representations
ROWNAMES<--method	Get feature names
rownames<--method	Get feature names
runEnrich	Functional enrichment analyses for dimensionally-reduced data
runEnrich-method	Functional enrichment analyses for dimensionally-reduced data
runICA	Run standard or stabilised Independent Component Analysis
runWGCNA	Run WGCNA for a data matrix
sampleNames	Get sample names
sampleNames-method	Get sample names
sampleNames<-	Get sample names
sampleNames<--method	Get sample names
show	Prints a summary of a ReducedExperiment object
show-method	Prints a summary of a ReducedExperiment object
slice	Extract and replace parts of ReducedExperiment objects
stability	Get and setting the stability values for factors
stability-method	Get and setting the stability values for factors
stability<-	Get and setting the stability values for factors
stability<--method	Get and setting the stability values for factors
[-method	Extract and replace parts of ReducedExperiment objects
[<--method	Extract and replace parts of ReducedExperiment objects