analyseDrugSetEnrichment {cTRAP} | R Documentation |
Analyse drug set enrichment
analyseDrugSetEnrichment( sets, stats, col = NULL, nperm = 10000, maxSize = 500, ..., keyColSets = NULL, keyColStats = NULL )
sets |
Named list of characters: named sets containing compound
identifiers (obtain drug sets by running |
stats |
Named numeric vector or either a |
col |
Character: name of the column to use for statistics (only required
if class of |
nperm |
Number of permutations to do. Minimial possible nominal p-value is about 1/nperm |
maxSize |
Maximal size of a gene set to test. All pathways above the threshold are excluded. |
... |
Arguments passed on to
|
keyColSets |
Character: column from |
keyColStats |
Character: column from |
Enrichment analysis based on GSEA
Other functions for drug set enrichment analysis:
loadDrugDescriptors()
,
plotDrugSetEnrichment()
,
prepareDrugSets()
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) analyseDrugSetEnrichment(drugSets, predicted)