prepareCMapPerturbations: Prepare CMap perturbation data

Description Usage Arguments Value See Also Examples

View source: R/CMap.R

Description

Prepare CMap perturbation data

Usage

1
2
3
4
5
6
7
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 matrix of perturbation z-scores? Not recommended in systems with less than 30GB of RAM; if FALSE, downstream functions will read the file chunk by chunk (this strategy impacts performance at the expense of a much 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

1
2
3
4
5
6
metadata <- loadCMapData("cmapMetadata.txt", "metadata")
metadata <- filterCMapMetadata(metadata, cellLine="HepG2")
## Not run: 
prepareCMapPerturbations(metadata, "cmapZscores.gctx", "cmapGeneInfo.txt")

## End(Not run)

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