prepareCMapPerturbations: Prepare CMap perturbation data

In cTRAP: Identification of candidate causal perturbations from differential gene expression 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)
loadZscores	Boolean: load matrix of perturbation z-scores? Not recommended in systems with less than 30GB of RAM; if FALSE, downstream functions will read the file chunk by chunk (this strategy impacts performance at the expense of a much 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)

cTRAP documentation built on Nov. 8, 2020, 10:58 p.m.