prepareCMapPerturbations {cTRAP} | R Documentation

## Prepare CMap perturbation data

### Description

Prepare CMap perturbation data

### Usage

    prepareCMapPerturbations(metadata, zscores, geneInfo,
      compoundInfo = NULL, loadZscores = FALSE)

### Arguments

`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

### Value

CMap perturbation data attributes and filename

### See Also

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`

### Examples

    ## Not run:
    metadata <- loadCMapData("cmapMetadata.txt", "metadata")
    metadata <- filterCMapMetadata(metadata, cellLine="HepG2")
    prepareCMapPerturbations(metadata, "cmapZscores.gctx", "cmapGeneInfo.txt")

    ## End(Not run)

[Package cTRAP version 1.5.0 Index]