plotDrugSetEnrichment {cTRAP}R Documentation

Plot drug set enrichment

Description

Plot drug set enrichment

Usage

plotDrugSetEnrichment(sets, stats, col = "rankProduct_rank",
  selectedSets = NULL)

Arguments

sets

Named list of characters: named sets containing compound identifiers (obtain drug sets by running prepareDrugSets())

stats

Named numeric vector or either a similarPerturbations or a targetingDrugs object (obtained after running rankSimilarPerturbations or predictTargetingDrugs, respectively)

col

Character: name of the column to use for statistics (only required if class of stats is either similarPerturbations or targetingDrugs)

selectedSets

Character: drug sets to plot (if NULL, plot all)

Value

List of GSEA plots per drug set

See Also

Other functions for drug set enrichment analysis: analyseDrugSetEnrichment, loadDrugDescriptors, prepareDrugSets

Examples

descriptors <- loadDrugDescriptors()
drugSets <- prepareDrugSets(descriptors)

# Analyse drug set enrichment in ranked targeting drugs for a differential
# expression profile
data("diffExprStat")
gdsc      <- loadExpressionDrugSensitivityAssociation("GDSC")
predicted <- predictTargetingDrugs(diffExprStat, gdsc)

plotDrugSetEnrichment(drugSets, predicted)
[Package cTRAP version 1.5.0 Index]