loadCMapData {cTRAP}R Documentation

Load CMap data

Description

Load CMap data (if not found, file will be automatically downloaded)

Usage

loadCMapData(file, type = c("metadata", "geneInfo", "zscores",
  "compoundInfo"), zscoresID = NULL)

Arguments

file

Character: path to file

type

Character: type of data to load (metadata, geneInfo, zscores or compoundInfo)

zscoresID

Character: identifiers to partially load z-scores file (for performance reasons; if NULL, all identifiers will be loaded)

Value

Metadata as a data table

Note

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.

See Also

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

Examples

# 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)


[Package cTRAP version 1.4.0 Index]