Package index • ReducedExperiment

All functions

assessSoftThreshold(): Assess soft thresholding power for WGCNA

associateComponents(): Runs linear models for components and sample-level data

calcEigengenes(<ModularExperiment>,<matrix>) calcEigengenes(<ModularExperiment>,<data.frame>) calcEigengenes(<ModularExperiment>,<SummarizedExperiment>) predict(<ModularExperiment>): Calculate eigengenes for new data

cbind(<FactorisedExperiment>) rbind(<FactorisedExperiment>) cbind(<ModularExperiment>) rbind(<ModularExperiment>) cbind(<ReducedExperiment>) rbind(<ReducedExperiment>): Combine ReducedExperiment objects by columns or rows

`componentNames<-`(<FactorisedExperiment>) `componentNames<-`(<ModularExperiment>) moduleNames(<ModularExperiment>) `moduleNames<-`(<ModularExperiment>) componentNames(<ReducedExperiment>) `componentNames<-`(<ReducedExperiment>): Get names of dimensionally-reduced components

dim(<ReducedExperiment>): Get the dimensions of a Reducedexperiment object

.DollarNames(<FactorisedExperiment>) .DollarNames(<ModularExperiment>) .DollarNames(<ReducedExperiment>): Command line completion for $

runEnrich(<FactorisedExperiment>) runEnrich(<ModularExperiment>): Functional enrichment analyses for dimensionally-reduced data

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

`names<-`(<FactorisedExperiment>) `featureNames<-`(<FactorisedExperiment>) `rownames<-`(<FactorisedExperiment>) `names<-`(<ModularExperiment>) `featureNames<-`(<ModularExperiment>) `rownames<-`(<ModularExperiment>) featureNames(<ReducedExperiment>) `names<-`(<ReducedExperiment>) `rownames<-`(<ReducedExperiment>) `ROWNAMES<-`(<ReducedExperiment>) `featureNames<-`(<ReducedExperiment>): Get feature names

getAlignedFeatures(<FactorisedExperiment>): Get feature alignments with factors

getCentrality(<ModularExperiment>): Get correlation of features with module eigengenes

getCommonFeatures(): Get common factor features

getMsigdbT2G(): Get TERM2GENE dataframe from MSigDB

getGeneIDs(<ReducedExperiment>): Gets alternative gene annotations from biomaRt

identifyModules(): Apply dimensionality reduction using Weighted Gene Correlation Network Analysis

nModules(<ModularExperiment>) nComponents(<ReducedExperiment>) nSamples(<ReducedExperiment>) nFeatures(<ReducedExperiment>): Prints individual lengths of samples, components and features

loadings(<FactorisedExperiment>) `loadings<-`(<FactorisedExperiment>) loadings(<ModularExperiment>) `loadings<-`(<ModularExperiment>): Get and set loadings

ModularExperiment(): ModularExperiment: A container for the results of module analysis

modulePreservation(): Get module preservation statistics

assignments(<ModularExperiment>) `assignments<-`(<ModularExperiment>): Get and set module feature assignments

dendrogram(<ModularExperiment>) `dendrogram<-`(<ModularExperiment>): Get the dendrogram stored in a ModularExperiment

plotCommonFeatures(): Heatmap comparing commonality across factors

plotDendro(<ModularExperiment>): Plot a dendrogram stored in a ModularExperiment

plotModulePreservation(): Plot module preservation statistics

plotStability(): Plot component stability as a function of the number of components

projectData(<FactorisedExperiment>,<matrix>) projectData(<FactorisedExperiment>,<data.frame>) projectData(<FactorisedExperiment>,<SummarizedExperiment>) predict(<FactorisedExperiment>): Project new data using pre-defined factors

reduced(<ReducedExperiment>) `reduced<-`(<ReducedExperiment>): Get and set reduced data

ReducedExperiment(): ReducedExperiment: A container for dimensionally-reduced representations

runICA(): Run standard or stabilised Independent Component Analysis

runWGCNA(): Run WGCNA for a data matrix

sampleNames(<ReducedExperiment>) `sampleNames<-`(<ReducedExperiment>) `colnames<-`(<ReducedExperiment>): Get sample names

show(<ReducedExperiment>): Prints a summary of a ReducedExperiment object

`[`(<FactorisedExperiment>,<ANY>,<ANY>,<ANY>) `[<-`(<FactorisedExperiment>,<ANY>,<ANY>,<FactorisedExperiment>) `[`(<ModularExperiment>,<ANY>,<ANY>,<ANY>) `[<-`(<ModularExperiment>,<ANY>,<ANY>,<ModularExperiment>) `[`(<ReducedExperiment>,<ANY>,<ANY>,<ANY>) `[<-`(<ReducedExperiment>,<ANY>,<ANY>,<ReducedExperiment>): Extract and replace parts of ReducedExperiment objects

stability(<FactorisedExperiment>) `stability<-`(<FactorisedExperiment>): Get and setting the stability values for factors