loadCMapZscores: Load matrix of CMap perturbation's differential expression...

In nuno-agostinho/cTRAP: Identification of candidate causal perturbations from differential gene expression data

Load matrix of CMap perturbation's differential expression z-scores (optional)

Description

Load matrix of CMap perturbation's differential expression z-scores (optional)

Usage

loadCMapZscores(data, inheritAttrs = FALSE, verbose = TRUE)

Arguments

data	perturbationChanges object
inheritAttrs	Boolean: convert to perturbationChanges object and inherit attributes from data?
verbose	Boolean: print additional details?

Value

Matrix containing CMap perturbation z-scores (genes as rows, perturbations as columns)

See Also

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

Examples

metadata <- loadCMapData("cmapMetadata.txt", "metadata")
metadata <- filterCMapMetadata(metadata, cellLine="HepG2")
## Not run: 
perts <- prepareCMapPerturbations(metadata, "cmapZscores.gctx",
                                  "cmapGeneInfo.txt")
zscores <- loadCMapZscores(perts[ , 1:10])

## End(Not run)

nuno-agostinho/cTRAP documentation built on March 28, 2024, 3:59 p.m.