Plot drug set enrichment
plotDrugSetEnrichment(
sets,
stats,
col = "rankProduct_rank",
selectedSets = NULL,
keyColSets = NULL,
keyColStats = NULL
)Named list of characters: named sets containing compound
identifiers (obtain drug sets by running prepareDrugSets())
Named numeric vector or either a similarPerturbations or
a targetingDrugs object (obtained after running
rankSimilarPerturbations or
predictTargetingDrugs, respectively)
Character: name of the column to use for statistics (only required
if class of stats is either similarPerturbations or
targetingDrugs)
Character: drug sets to plot (if NULL, plot all)
Character: column from sets to compare with column
keyColStats from stats; automatically selected if NULL
Character: column from stats to compare with column
keyColSets from sets; automatically selected if NULL
List of GSEA plots per drug set
Other functions for drug set enrichment analysis:
analyseDrugSetEnrichment(),
loadDrugDescriptors(),
prepareDrugSets()
descriptors <- loadDrugDescriptors()
drugSets <- prepareDrugSets(descriptors)
# Analyse drug set enrichment in ranked targeting drugs for a differential
# expression profile
data("diffExprStat")
gdsc <- loadExpressionDrugSensitivityAssociation("GDSC")
#> Loading data from expressionDrugSensitivityCorGDSC7.qs...
#> Error in qread(file): Malformed compress block: compressed size > compress bound
predicted <- predictTargetingDrugs(diffExprStat, gdsc)
#> Error in predictTargetingDrugs(diffExprStat, gdsc): object 'gdsc' not found
plotDrugSetEnrichment(drugSets, predicted)
#> Matching compounds with those available in drug sets...
#> Error in prepareStatsCol(col, stats): object 'predicted' not found