Load matrix of CMap perturbation's differential expression z-scores (optional) — loadCMapZscores • cTRAP

Load matrix of CMap perturbation's differential expression z-scores (optional)

loadCMapZscores(data, inheritAttrs = FALSE, verbose = TRUE)

Arguments

data: perturbationChanges object
inheritAttrs: Boolean: convert to perturbationChanges object and inherit attributes from data?
verbose: Boolean: print additional details?

Value

Matrix containing CMap perturbation z-scores (genes as rows, perturbations as columns)

See also

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

Examples

metadata <- loadCMapData("cmapMetadata.txt", "metadata")
#> Loading CMap metadata from cmapMetadata.txt...
metadata <- filterCMapMetadata(metadata, cellLine="HepG2")
if (FALSE) {
perts <- prepareCMapPerturbations(metadata, "cmapZscores.gctx",
                                  "cmapGeneInfo.txt")
zscores <- loadCMapZscores(perts[ , 1:10])
}