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)
`...` | Arguments passed on to `filterCMapMetadata` `cellLine` Character: cell line (if `NULL`, all values are loaded) `timepoint` Character: timepoint (if `NULL`, all values are loaded) `dosage` Character: dosage (if `NULL`, all values are loaded) `perturbationType` Character: type of perturbation (if `NULL`, all perturbation types are loaded)
`loadZscores` | Boolean: load matrix of perturbation z-scores? Not recommended in systems with less than 30GB of RAM; if `FALSE`, downstream functions will load and process the file directly chunk by chunk, resulting in a lower memory footprint

### Value

CMap perturbation data attributes and filename

### See Also

Other functions related with the ranking of CMap perturbations: `as.table.referenceComparison()`, `filterCMapMetadata()`, `getCMapConditions()`, `getCMapPerturbationTypes()`, `loadCMapData()`, `loadCMapZscores()`, `parseCMapID()`, `plot.perturbationChanges()`, `plot.referenceComparison()`, `plotTargetingDrugsVSsimilarPerturbations()`, `print.similarPerturbations()`, `rankSimilarPerturbations()`

### Examples

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

    ## End(Not run)

[Package cTRAP version 1.12.0 Index]