loadL1000perturbations {cTRAP}R Documentation

Load L1000 perturbation data

Description

Load L1000 perturbation data

Usage

loadL1000perturbations(metadata, zscores, geneInfo,
  sanitizeCompoundNames = FALSE)

Arguments

metadata

Data frame: L1000 Metadata

zscores

Data frame: GCTX z-scores

geneInfo

Data frame: L1000 gene info

sanitizeCompoundNames

Boolean: replace identifiers with compound names

Value

Perturbation data from L1000 as a data table

Examples

if (interactive()) {
  metadata <- downloadL1000data("l1000metadata.txt", "metadata")
  metadata <- filterL1000metadata(metadata, cellLine="HepG2")
  zscores  <- downloadL1000data("l1000zscores.gctx", "zscores",
      metadata$sig_id)
  geneInfo <- downloadL1000data("l1000geneInfo.txt", "geneInfo")
  loadL1000perturbations(metadata, zscores, geneInfo)
}

[Package cTRAP version 1.2.0 Index]