cmapPerturbationsKD {cTRAP} | R Documentation

## CMap perturbations sample for knockdown experiments

### Description

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

    # Code for loading CMap gene KD HepG2 data
    cellLine <- "HepG2"
    cmapMetadataKD <- filterCMapMetadata(
      "cmapMetadata.txt", cellLine=cellLine,
      perturbationType="Consensus signature from shRNAs targeting the same gene")

    cmapPerturbationsKD <- prepareCMapPerturbations(
      cmapMetadataKD, "cmapZscores.gctx", "cmapGeneInfo.txt",
      loadZscores=TRUE)

    data("diffExprStat")
    compareKD <- rankSimilarPerturbations(diffExprStat, cmapPerturbationsKD)

    # Select only some perturbations (to reduce file size)
    filter <- c(head(order(compareKD$spearman_rank)),
                tail(order(compareKD$spearman_rank)),
                head(order(compareKD$pearson_rank)),
                tail(order(compareKD$pearson_rank)),
                head(order(compareKD$gsea_rank)),
                tail(order(compareKD$gsea_rank)))
    filter <- unique(compareKD[[1]][filter])
    cmapPerturbationsKD <- cmapPerturbationsKD[ , filter]

    # Remove non-ASCII characters for portability reasons
    metadata <- attr(cmapPerturbationsKD, "metadata")
    metadata$pert_idose <- gsub("\u00B5", "micro", metadata$pert_idose)
    metadata$pert_dose_unit <- gsub("\u00B5", "micro", metadata$pert_dose_unit)
    attr(cmapPerturbationsKD, "metadata") <- metadata

[Package cTRAP version 1.5.0 Index]