getCMapConditions: List available conditions in CMap datasets

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

List available conditions in CMap datasets

Description

Downloads metadata if not available

Usage

getCMapConditions(
  metadata,
  cellLine = NULL,
  timepoint = NULL,
  dosage = NULL,
  perturbationType = NULL,
  control = FALSE
)

Arguments

metadata	Data frame (CMap metadata) or character (respective filepath)
cellLine	Character: cell line (if NULL, all values are loaded)
timepoint	Character: timepoint (if NULL, all values are loaded)
dosage	Character: dosage (if NULL, all values are loaded)
perturbationType	Character: type of perturbation (if NULL, all perturbation types are loaded)
control	Boolean: show controls for perturbation types?

Value

List of conditions in CMap datasets

See Also

Other functions related with the ranking of CMap perturbations: as.table.referenceComparison(), filterCMapMetadata(), getCMapPerturbationTypes(), loadCMapData(), loadCMapZscores(), parseCMapID(), plot.perturbationChanges(), plot.referenceComparison(), plotTargetingDrugsVSsimilarPerturbations(), prepareCMapPerturbations(), print.similarPerturbations(), rankSimilarPerturbations()

Examples

## Not run: 
cmapMetadata <- loadCMapData("cmapMetadata.txt", "metadata")

## End(Not run)
getCMapConditions(cmapMetadata)

nuno-agostinho/cTRAP documentation built on Jan. 2, 2025, 12:11 a.m.