plotDrugSetEnrichment {cTRAP} | R Documentation

## 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)

[Package cTRAP version 1.12.0 Index]