downloadL1000data {cTRAP}R Documentation

Download L1000 data

Description

The data will be downloaded if not available

Usage

downloadL1000data(file, type = c("metadata", "geneInfo", "zscores"),
  zscoresId = NULL)

Arguments

file

Character: filepath

type

Character: type of data to load

zscoresId

Character: identifiers to partially load z-scores file (for performance reasons)

Value

Metadata as a data table

Examples

# Download L1000 metadata
l1000metadata <- downloadL1000data("l1000metadata.txt", "metadata")

# Download L1000 gene info
downloadL1000data("l1000geneInfo.txt", "geneInfo")

# Download L1000 zscores based on filtered metadata
l1000metadataKnockdown <- filterL1000metadata(
  l1000metadata, cellLine="HepG2",
  perturbationType="Consensus signature from shRNAs targeting the same gene")

if (interactive()) {
    downloadL1000data("l1000zscores.gctx.gz", "zscores",
                      l1000metadataKnockdown$sig_id)
}

[Package cTRAP version 1.2.0 Index]