l1000perturbationsSmallMolecules {cTRAP} | R Documentation

## L1000 perturbations sample for small molecules

### Description

L1000 perturbations sample for small molecules obtained by running the following code:

    l1000metadataSmallMolecules <- filterL1000metadata(
        l1000metadata, cellLine="HepG2", timepoint="24 h",
        dosage="5 \U00B5M", # \U00B5 is the unicode code for the micro symbol
        perturbationType="Compound")
    l1000zscores  <- downloadL1000data("l1000zscores.gctx", "zscores",
                                       l1000metadataSmallMolecules$sig_id)
    l1000geneInfo <- downloadL1000data("l1000geneInfo.txt")

    l1000perturbationsSmallMolecules <- loadL1000perturbations(
        l1000metadataSmallMolecules, l1000zscores, l1000geneInfo,
        sanitizeCompoundNames=TRUE)

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

    compareSmallMolecule <- list()
    compareSmallMolecule$spearman <- compareAgainstL1000(
        diffExprStat, l1000perturbationsSmallMolecules, cellLine,
        method="spearman")
    compareSmallMolecule$pearson <- compareAgainstL1000(
        diffExprStat, l1000perturbationsSmallMolecules, cellLine,
        method="pearson")
    compareSmallMolecule$gsea <- compareAgainstL1000(
        diffExprStat, l1000perturbationsSmallMolecules, cellLine, method="gsea",
        geneSize=150)

    genes  <- lapply(compareSmallMolecule, "[[", "genes")
    filter <- c(unlist(lapply(genes, head)), unlist(lapply(genes, tail)))
    l1000perturbationsSmallMolecules <- l1000perturbationsSmallMolecules[
        , filter]

[Package cTRAP version 1.0.3 Index]