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)