analyseDrugSetEnrichment {cTRAP}R Documentation

Analyse drug set enrichment

Description

Analyse drug set enrichment

Usage

analyseDrugSetEnrichment(sets, stats, col = NULL, nperm = 10000,
  maxSize = 500, ...)

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)

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 fgsea::fgsea

minSize

Minimal size of a gene set to test. All pathways below the threshold are excluded.

nproc

If not equal to zero sets BPPARAM to use nproc workers (default = 0).

gseaParam

GSEA parameter value, all gene-level statis are raised to the power of 'gseaParam' before calculation of GSEA enrichment scores.

BPPARAM

Parallelization parameter used in bplapply. Can be used to specify cluster to run. If not initialized explicitly or by setting 'nproc' default value 'bpparam()' is used.

Value

Enrichment analysis based on GSEA

See Also

Other functions for drug set enrichment analysis: loadDrugDescriptors, plotDrugSetEnrichment, 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)

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