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: `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")
    ## 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)

[Package cTRAP version 1.12.0 Index]