inst/scripts/make-metadata_21Q2.R

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

### =========================================================================
### depmap metadata 21Q2 data 
### -------------------------------------------------------------------------
### this script generates the metadata_21Q2.csv
## note: this script assumes that your current directory is depmap/inst/scripts/
## https://depmap.org/portal/download/

data.frame(
    Title = c(paste0("crispr_21Q2"), 
              paste0("copyNumber_21Q2"),
              paste0("TPM_21Q2"),
              paste0("mutationCalls_21Q2"),
              paste0("metadata_21Q2")),
    Description = c(
        paste0("(CERES) Batch and off-target corrected CRISPR-Cas9 gene, ",
               "knockdout dependency data for 17645 genes, 990 cell lines, 32 ",
               "primary diseases and 30 lineages."),
        paste0("WES log copy number data for 27562 genes, 1742 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 19177 genes, 1379 cell lines, 33 primary diseases ",
               "and 37 lineages."),
        paste0("CCLE mutation calls (for coding region, germline filtered) ",
               "and includes data from 18787 genes, 1750 cell lines, 35 ", 
               "primary diseases and 38 lineages."),
        paste0("Metadata for cell lines in the 21Q2 DepMap release, for 0 ",
               "genes, 1814 cell lines, 35 primary diseases and 39 lineages.")),
    BiocVersion = "3.13",
    Genome = "", 
    SourceType = "CSV",
    SourceUrl = c(paste0("https://ndownloader.figshare.com/files/27902226"),
                  paste0("https://ndownloader.figshare.com/files/27902124"),
                  paste0("https://ndownloader.figshare.com/files/27902091"),
                  paste0("https://ndownloader.figshare.com/files/27902118"),
                  paste0("https://ndownloader.figshare.com/files/27902376")),
    SourceVersion = "May 27 2021",
    Species = "Homo sapiens",
    TaxonomyId = 9606,
    Coordinate_1_based = TRUE,
    DataProvider = "Broad Institute",
    Maintainer = "Theo Killian <theo.killian@kuleuven.be>",
    RDataClass = "tibble",
    DispatchClass = "Rda",
    RDataPath = c(paste0("depmap/crispr_21Q2.rda"),
                  paste0("depmap/copyNumber_21Q2.rda"),
                  paste0("depmap/TPM_21Q2.rda"),
                  paste0("depmap/mutationCalls_21Q2.rda"),
                  paste0("depmap/metadata_21Q2.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 21Q2 release") -> meta_21Q2

write.csv(meta_21Q2, file = "../extdata/metadata_21Q2.csv", row.names = FALSE)
## to upload this metadata to EH, enter the following into the CL
# ExperimentHubData::makeExperimentHubMetadata("~/tmp/21Q2/depmap/",
#                                              fileName = "metadata_21Q2.csv")