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:
as.table.referenceComparison()
,
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") ## Not run: # 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) ## End(Not run)