inst/scripts/make-metadata_20Q4.R

In UCLouvain-CBIO/depmap: Cancer Dependency Map Data Package

### =========================================================================
### depmap metadata 20Q4 data 
### -------------------------------------------------------------------------
### this script generates the metadata_20Q4.csv
## note: this script assumes that your current directory is depmap/inst/scripts/
## https://depmap.org/portal/download/

meta_20Q4 <- data.frame(
    Title = c(paste0("crispr_20Q4"), 
              paste0("copyNumber_20Q4"),
              paste0("TPM_20Q4"),
              paste0("mutationCalls_20Q4"),
              paste0("metadata_20Q4")),
    Description = c(
        paste0("(CERES) Batch and off-target corrected CRISPR-Cas9 gene, ",
               "knockdout dependency data for 18119 genes, 808 cell lines, 31 ",
               "primary diseases and 29 lineages."), 
        paste0("WES log copy number data for 27562 genes, 1753 cell lines, 35 ",
               "primary diseases and 38 lineages."),
        paste0("CCLE 'Transcript Per Million' (TPM) RNAseq gene expression ",
               "data (in scale scale (log2(TPM+1))) for protein coding genes ",
               "from 19182 genes, 1376 cancer cell lines, 33 primary diseases ",
               "and 37 lineages."), 
        paste0("CCLE mutation calls (for coding region, germline filtered) ",
               "and includes data from 18789 genes, 1749 cell lines, 35 ", 
               "primary diseases and 38 lineages. "),
        paste0("Metadata for cell lines in the 20Q4 DepMap release, for 0 ",
               "genes, 1812 cell lines, 35 primary diseases and 39 lineages.")),
    BiocVersion = "3.12",
    Genome = "", 
    SourceType = "CSV", 
    SourceUrl = c(paste0("https://ndownloader.figshare.com/files/25494359"),
                  paste0("https://ndownloader.figshare.com/files/25494416"),
                  paste0("https://ndownloader.figshare.com/files/25494389"),
                  paste0("https://ndownloader.figshare.com/files/25494419"),
                  paste0("https://ndownloader.figshare.com/files/25494443")),
    SourceVersion = "Nov 20 2020",
    Species = "Homo sapiens",
    TaxonomyId = 9606,
    Coordinate_1_based = TRUE,
    DataProvider = "Broad Institute",
    Maintainer = "Theo Killian <theodore.killian@kuleuven.vib.be>",
    RDataClass = "tibble",
    DispatchClass = "Rda",
    RDataPath = c(paste0("depmap/crispr_20Q4.rda"), 
                  paste0("depmap/copyNumber_20Q4.rda"),
                  paste0("depmap/TPM_20Q4.rda"),
                  paste0("depmap/mutationCalls_20Q4.rda"),
                  paste0("depmap/metadata_20Q4.rda")),
    Tags = paste0("ExperimentHub, ExperimentData, ReproducibleResearch, RepositoryData, AssayDomainData, ", 
                "CopyNumberVariationData, DiseaseModel, CancerData, BreastCancerData, ColonCancerData, ", 
                "KidneyCancerData, LeukemiaCancerData, LungCancerData, OvarianCancerData, ProstateCancerData", 
                "OrganismData, Homo_sapiens_Data, PackageTypeData, SpecimenSource, CellCulture, Genome, ", 
                "Proteome, StemCell, Tissue"),
    Notes = "This dataset is from the 20Q4 release")

write.csv(meta_20Q4, file = "../extdata/metadata_20Q4.csv", row.names = FALSE)
## to upload this metadata to EH, enter the following into the CL
## ExperimentHubData::makeExperimentHubMetadata("~/tmp/depmap/", fileName = "metadata_20Q4.csv")