| 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) |
... |
Arguments passed on to
|
loadZscores |
Boolean: load matrix of perturbation z-scores? Not
recommended in systems with less than 30GB of RAM; if |
CMap perturbation data attributes and filename
Other functions related with the ranking of CMap perturbations:
as.table.referenceComparison(),
filterCMapMetadata(),
getCMapConditions(),
getCMapPerturbationTypes(),
loadCMapData(),
loadCMapZscores(),
parseCMapID(),
plot.perturbationChanges(),
plot.referenceComparison(),
plotTargetingDrugsVSsimilarPerturbations(),
print.similarPerturbations(),
rankSimilarPerturbations()
metadata <- loadCMapData("cmapMetadata.txt", "metadata")
metadata <- filterCMapMetadata(metadata, cellLine="HepG2")
## Not run:
prepareCMapPerturbations(metadata, "cmapZscores.gctx", "cmapGeneInfo.txt")
## End(Not run)