# Identification of candidate causal perturbations from differential gene expression data

## Documentation for package ‘cTRAP’ version 1.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

cTRAP-package | cTRAP package
analyseDrugSetEnrichment | Analyse drug set enrichment
as.table.similarPerturbations | Cross Tabulation and Table Creation
compareAgainstCMap | Rank CMap perturbations' similarity to a differential expression profile
compareAgainstReference | Compare multiple methods and rank reference accordingly
convertENSEMBLtoGeneSymbols | Convert ENSEMBL gene identifiers to gene symbols
cTRAP | cTRAP package
dim.perturbationChanges | Dimensions of a 'perturbationChanges' object
dimnames.perturbationChanges | Dimnames of a 'perturbationChanges' object
downloadENCODEknockdownMetadata | Download metadata for ENCODE knockdown experiments
filterCMapMetadata | Filter CMap metadata
getCMapConditions | List available conditions in CMap datasets
getCMapPerturbationTypes | Get perturbation types
loadCMapData | Load CMap data
loadCMapZscores | Load matrix of CMap perturbation's differential expression z-scores
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 | Plot perturbation comparison against a differential expression profile
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 an ENCODE gene expression data
print.similarPerturbations | Print a 'similarPerturbations' object
rankSimilarPerturbations | Rank CMap perturbations' similarity to a differential expression profile
[.perturbationChanges | Subset a 'perturbationChanges' object