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]