inst/scripts/make-metadata_20Q2.R

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

### =========================================================================
### depmap metadata 20Q2 data 
### -------------------------------------------------------------------------
### this script generates the metadata_20Q2.csv
## note: this script assumes that your current directory is depmap/inst/scripts/

meta_20Q2 <- data.frame(
    Title = c(paste0("crispr_20Q2"), 
              paste0("copyNumber_20Q2"),
              paste0("TPM_20Q2"),
              paste0("mutationCalls_20Q2"),
              paste0("metadata_20Q2"),
              paste0("proteomic_20Q2")),
    Description = c( paste0("(CERES) Batch and off-target corrected CRISPR-Cas9 ", 
                           "gene knockdout dependency data for 18119 genes, ", 
                           "769 cell lines, 29 primary diseases and 26 ", 
                           "lineages."), 
                    paste0("WES log copy number data for 27639 genes, 1745 ", 
                           "cell lines, 35 primary diseases and 37 lineages."),
                    paste0("CCLE 'Transcript Per Million' (TPM) RNAseq gene ", 
                           "expression data (in scale scale (log2(TPM+1))) ", 
                           "for protein coding genes from 19144 genes, 1304 ", 
                           "cancer cell lines, 32 primary diseases and 34 ", 
                           "lineages."), 
                    paste0("Merged mutation calls (for coding region, germline ", 
                           "filtered) and includes data from 18802 genes, 1741 ", 
                           "cell lines, 35 primary diseases and 37 lineages. "),
                    paste0("Metadata for cell lines in the 20Q2 DepMap release, ", 
                           "for 0 genes, 1804 cell lines, 35 primary diseases ", 
                           "and 38 lineages."),
                    paste0("Quantitative profiling of 12399 proteins in 375 cell ",
                           "lines, 24 primary diseases and 27 lineages by mass ",
                           "spectrometry across 375 cell lines from the Gygi lab.")),
    BiocVersion = "3.12",
    Genome = "", 
    SourceType = "CSV", 
    SourceUrl = c(paste0("https://ndownloader.figshare.com/files/22629068"),
                  paste0("https://ndownloader.figshare.com/files/22629107"),
                  paste0("https://ndownloader.figshare.com/files/22629092"),
                  paste0("https://ndownloader.figshare.com/files/22629110"),
                  paste0("https://ndownloader.figshare.com/files/22629137"),
                  paste0("https://gygi.med.harvard.edu/sites/gygi.med.harvard.edu/files/documents/protein_quant_current_normalized.csv.gz")),
    SourceVersion = "May 15 2020",
    Species = "Homo sapiens",
    TaxonomyId = 9606,
    Coordinate_1_based = TRUE,
    DataProvider = "Broad Institute",
    Maintainer = "Theo Killian <theodore.killian@uclouvain.be>",
    RDataClass = "tibble",
    DispatchClass = "Rda",
    RDataPath = c(paste0("depmap/crispr_20Q2.rda"), 
                  paste0("depmap/copyNumber_20Q2.rda"),
                  paste0("depmap/TPM_20Q2.rda"),
                  paste0("depmap/mutationCalls_20Q2.rda"),
                  paste0("depmap/metadata_20Q2.rda"),
                  paste0("depmap/proteomic_20Q2.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 20Q2 release")

write.csv(meta_20Q2, file = "../extdata/metadata_20Q2.csv", row.names = FALSE)
## to upload this metadata to EH, enter the following into the CL
## ExperimentHubData::makeExperimentHubMetadata("~/tmp/depmap/", fileName = "metadata_20Q2.csv")