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]