Analyse drug set enrichment

Analyse drug set enrichment

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

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::fgseaSimple

minSize

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

scoreType

This parameter defines the GSEA score type. Possible options are ("std", "pos", "neg")

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.

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

Enrichment analysis based on GSEA

See also

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

Examples

descriptors <- loadDrugDescriptors()
#> compound_descriptors_NCI60_2D.qs not found: downloading data...
drugSets <- prepareDrugSets(descriptors)

# Analyse drug set enrichment in ranked targeting drugs for a differential
# expression profile
data("diffExprStat")
gdsc      <- loadExpressionDrugSensitivityAssociation("GDSC")
#> expressionDrugSensitivityCorGDSC7.qs not found: downloading data...
#> Warning: URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs': Timeout of 60 seconds was reached
#> Error in download.file(link, file, mode = mode): download from 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs' failed
predicted <- predictTargetingDrugs(diffExprStat, gdsc)
#> Error in predictTargetingDrugs(diffExprStat, gdsc): object 'gdsc' not found

analyseDrugSetEnrichment(drugSets, predicted)
#> Matching compounds with those available in drug sets...
#> Error in prepareStatsCol(col, stats): object 'predicted' not found