| loadCMapData {cTRAP} | R Documentation |
Load CMap data (if not found, file will be automatically downloaded)
loadCMapData(file, type = c("metadata", "geneInfo", "zscores",
"compoundInfo"), zscoresID = NULL)
file |
Character: path to file |
type |
Character: type of data to load ( |
zscoresID |
Character: identifiers to partially load z-scores file
(for performance reasons; if |
Metadata as a data table
If type = "compoundInfo", two files from
The Drug Repurposing Hub will be downloaded containing information
about drugs and perturbations. The files will be named file with
_drugs and _samples before their extension, respectively.
Other functions related with the ranking of CMap perturbations: [.perturbationChanges,
as.table.similarPerturbations,
dim.perturbationChanges,
dimnames.perturbationChanges,
filterCMapMetadata,
getCMapConditions,
getCMapPerturbationTypes,
loadCMapZscores, parseCMapID,
plot.perturbationChanges,
plot.referenceComparison,
plotTargetingDrugsVSsimilarPerturbations,
prepareCMapPerturbations,
print.similarPerturbations,
rankSimilarPerturbations
# Load CMap metadata (data is automatically downloaded if not available)
cmapMetadata <- loadCMapData("cmapMetadata.txt", "metadata")
# Load CMap gene info
loadCMapData("cmapGeneInfo.txt", "geneInfo")
# Load CMap zscores based on filtered metadata
cmapMetadataKnockdown <- filterCMapMetadata(
cmapMetadata, cellLine="HepG2",
perturbationType="Consensus signature from shRNAs targeting the same gene")
loadCMapData("cmapZscores.gctx.gz", "zscores", cmapMetadataKnockdown$sig_id)