l1000perturbationsKnockdown {cTRAP} | R Documentation

## L1000 perturbations sample for knockdown experiments

### Description

L1000 perturbations sample for knockdown experiments obtained by running the following code:

    # Code for loading CMap gene KD HepG2 data
    l1000metadata <- downloadL1000data("l1000metadata.txt", "metadata")
    l1000metadataKnockdown <- filterL1000metadata(
      l1000metadata, cellLine="HepG2",
      perturbationType="Consensus signature from shRNAs targeting the same gene")
    l1000zscores  <- downloadL1000data("l1000zscores.gctx", "zscores",
                                       l1000metadataKnockdown$sig_id)
    l1000geneInfo <- downloadL1000data("l1000geneInfo.txt", "geneInfo")

    l1000perturbationsKnockdown <- loadL1000perturbations(
      l1000metadataKnockdown, l1000zscores, l1000geneInfo)

    # Select only some perturbations (to reduce file size)
    data("diffExprStat")

    compareKnockdown <- list()
    compareKnockdown$spearman <- compareAgainstL1000(
        diffExprStat, l1000perturbationsKnockdown, cellLine, method="spearman")
    compareKnockdown$pearson <- compareAgainstL1000(
        diffExprStat, l1000perturbationsKnockdown, cellLine, method="pearson")
    compareKnockdown$gsea <- compareAgainstL1000(
        diffExprStat, l1000perturbationsKnockdown, cellLine, method="gsea",
        geneSize=150)

    genes  <- lapply(compareKnockdown, "[[", "genes")
    filter <- c(unlist(lapply(genes, head)), unlist(lapply(genes, tail)))
    l1000perturbationsKnockdown <- l1000perturbationsKnockdown[ , filter]

[Package cTRAP version 1.2.0 Index]