plotDrugSetEnrichment: Plot drug set enrichment

In nuno-agostinho/cTRAP: Identification of candidate causal perturbations from differential gene expression data

Plot drug set enrichment

Description

Plot drug set enrichment

Usage

plotDrugSetEnrichment(
  sets,
  stats,
  col = "rankProduct_rank",
  selectedSets = NULL,
  keyColSets = NULL,
  keyColStats = 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)
keyColSets	Character: column from sets to compare with column keyColStats from stats; automatically selected if NULL
keyColStats	Character: column from stats to compare with column keyColSets from sets; automatically selected if NULL

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)

nuno-agostinho/cTRAP documentation built on March 28, 2024, 3:59 p.m.