loadCMapData: Load CMap data

In cTRAP: Identification of candidate causal perturbations from differential gene expression 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: as.table.referenceComparison(), 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)

cTRAP documentation built on Nov. 8, 2020, 10:58 p.m.