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