| prepareCMapPerturbations {cTRAP} | R Documentation |
Prepare CMap perturbation data
prepareCMapPerturbations(metadata, zscores, geneInfo, compoundInfo = NULL, loadZscores = FALSE)
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 perturbation z-scores? Not recommended in memory-constrained systems |
CMap perturbation data attributes and filename
Other functions related with the ranking of CMap perturbations: [.perturbationChanges,
as.table.similarPerturbations,
dim.perturbationChanges,
dimnames.perturbationChanges,
filterCMapMetadata,
getCMapConditions,
getCMapPerturbationTypes,
loadCMapData,
loadCMapZscores, parseCMapID,
plot.perturbationChanges,
plot.referenceComparison,
plotTargetingDrugsVSsimilarPerturbations,
print.similarPerturbations,
rankSimilarPerturbations
## Not run:
metadata <- loadCMapData("cmapMetadata.txt", "metadata")
metadata <- filterCMapMetadata(metadata, cellLine="HepG2")
prepareCMapPerturbations(metadata, "cmapZscores.gctx", "cmapGeneInfo.txt")
## End(Not run)