Identification of candidate causal perturbations from differential gene expression data

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Documentation for package ‘cTRAP’ version 1.8.0

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