# Containers and tools for dimensionally-reduced -omics representations

## Documentation for package ‘ReducedExperiment’ version 1.2.0

- 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