prepareCMapPerturbations: Prepare CMap perturbation data

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

Prepare CMap perturbation data

Description

Prepare CMap perturbation data

Usage

prepareCMapPerturbations(
  metadata,
  zscores,
  geneInfo,
  compoundInfo = NULL,
  ...,
  loadZscores = FALSE
)

Arguments

metadata	Data frame (CMap metadata) or character (respective filepath to load data from file)
zscores	Data frame (GCTX z-scores) or character (respective filepath to load data from file)
geneInfo	Data frame (CMap gene info) or character (respective filepath to load data from file)
compoundInfo	Data frame (CMap compound info) or character (respective filepath to load data from file)
...	Arguments passed on to filterCMapMetadata 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)
loadZscores	Boolean: load matrix of perturbation z-scores? Not recommended in systems with less than 30GB of RAM; if FALSE, downstream functions will load and process the file directly chunk by chunk, resulting in a lower memory footprint

Value

CMap perturbation data attributes and filename

See Also

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

Examples

metadata <- loadCMapData("cmapMetadata.txt", "metadata")
metadata <- filterCMapMetadata(metadata, cellLine="HepG2")
## Not run: 
prepareCMapPerturbations(metadata, "cmapZscores.gctx", "cmapGeneInfo.txt")

## End(Not run)

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