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)