l1000perturbationsKnockdown {cTRAP} | R Documentation |
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]