cmapPerturbationsCompounds {cTRAP} | R Documentation

## CMap perturbations sample for small molecules

### Description

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

    cellLine <- c("HepG2", "HUH7")
    cmapMetadataCompounds <- filterCMapMetadata(
        "cmapMetadata.txt", cellLine=cellLine, timepoint="24 h",
        dosage="5 \u00B5M", perturbationType="Compound")

    cmapPerturbationsCompounds <- prepareCMapPerturbations(
        cmapMetadataCompounds, "cmapZscores.gctx", "cmapGeneInfo.txt",
        "cmapCompoundInfo_drugs.txt", loadZscores=TRUE)

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

[Package cTRAP version 1.12.0 Index]