Package index • cTRAP

Interactive functions
`launchDiffExprLoader()`	Load differential expression data via a visual interface
`launchCMapDataLoader()`	Load CMap data via a visual interface
`launchResultPlotter()`	View and plot results via a visual interface
`launchMetadataViewer()`	View metadata via a visual interface
`launchDrugSetEnrichmentAnalyser()`	View and plot results via a visual interface
`cTRAP()`	cTRAP package
Prepare ENCODE data
`downloadENCODEknockdownMetadata()`	Download metadata for ENCODE knockdown experiments
`loadENCODEsamples()`	Load ENCODE samples
`prepareENCODEgeneExpression()`	Load ENCODE gene expression data
`convertENSEMBLtoGeneSymbols()`	Convert ENSEMBL gene identifiers to gene symbols
`performDifferentialExpression()`	Perform differential gene expression based on ENCODE data
Download and manipulate CMap perturbation data
`getCMapConditions()`	List available conditions in CMap datasets
`getCMapPerturbationTypes()`	Get CMap perturbation types
`loadCMapData()`	Load CMap data
`loadCMapZscores()`	Load matrix of CMap perturbation's differential expression z-scores (optional)
`filterCMapMetadata()`	Filter CMap metadata
`prepareCMapPerturbations()`	Prepare CMap perturbation data
`plot(<perturbationChanges>)` `[`(<perturbationChanges>) `dim(<perturbationChanges>)` `dimnames(<perturbationChanges>)`	Operations on a `perturbationChanges` object
`parseCMapID()`	Parse CMap identifier
Rank similar CMap perturbations
`rankSimilarPerturbations()`	Rank differential expression profile against CMap perturbations by similarity
`plot(<referenceComparison>)`	Plot data comparison
`as.table(<referenceComparison>)`	Cross Tabulation and Table Creation
`plotTargetingDrugsVSsimilarPerturbations()`	Plot similar perturbations against predicted targeting drugs
`print(<similarPerturbations>)`	Print a `similarPerturbations` object
Predict targeting drugs
`listExpressionDrugSensitivityAssociation()`	List available gene expression and drug sensitivity correlation matrices
`loadExpressionDrugSensitivityAssociation()`	Load gene expression and drug sensitivity correlation matrix
`dimnames(<expressionDrugSensitivityAssociation>)` `dim(<expressionDrugSensitivityAssociation>)` `[`(<expressionDrugSensitivityAssociation>)	Operations on `expressionDrugSensitivityAssociation` objects
`predictTargetingDrugs()`	Predict targeting drugs
`plot(<referenceComparison>)`	Plot data comparison
`as.table(<referenceComparison>)`	Cross Tabulation and Table Creation
`plotTargetingDrugsVSsimilarPerturbations()`	Plot similar perturbations against predicted targeting drugs
Analyse drug (descriptor) set enrichment
`loadDrugDescriptors()`	Load table with drug descriptors
`prepareDrugSets()`	Prepare drug sets from a table with compound descriptors
`analyseDrugSetEnrichment()`	Analyse drug set enrichment
`plotDrugSetEnrichment()`	Plot drug set enrichment

Reference

Interactive functions

Prepare ENCODE data

Download and manipulate CMap perturbation data

Rank similar CMap perturbations

Predict targeting drugs

Analyse drug (descriptor) set enrichment