inst/scripts/make-metadata_19Q1.R

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

### =========================================================================
### depmap metadata 19Q1 data
### -------------------------------------------------------------------------
### this script generates the metadata_19Q1.csv
## note: this script assumes that your current directory is depmap/inst/scripts/

meta_19Q1 <- data.frame(
    Title = c(paste0("rnai_19Q1"),
              paste0("crispr_19Q1"), 
              paste0("copyNumber_19Q1"),
              paste0("RPPA_19Q1"), 
              paste0("TPM_19Q1"),
              paste0("mutationCalls_19Q1"),
              paste0("metadata_19Q1")),
    Description = c(paste0("(DEMETER2) Batch and off-target corrected RNAi ", 
                           "gene knockdown dependency data for 17309 genes, ", 
                           "711 cancer cell lines, 30 primary Diseases and ", 
                           "31 lineages."), 
                    paste0("(CERES) Batch and off-target corrected CRISPR-Cas9 ", 
                           "gene knockdout dependency data for 17634 genes, ", 
                           "558 cell lines, 26 primary diseases and 28 ", 
                           "lineages."), 
                    paste0("WES log copy number data for 23299 genes, 1604 ", 
                           "cell lines, 38 primary diseases and 33 lineages."),
                    paste0("Reverse Phase Protein Array (RPPA) Western Blot ", 
                           "expression data from 214 genes, 899 cancer cell ", 
                           "lines, 28 primary diseases and 28 lineages."),
                    paste0("CCLE 'Transcript Per Million' (TPM) RNAseq gene ", 
                           "expression data (in scale scale (log2(TPM+1))) ", 
                           "for protein coding genes from 57820 genes, 1165 ", 
                           "cancer cell lines, 33 primary diseases and 32 ", 
                           "lineages."), 
                    paste0("Merged mutation calls (for coding region, germline ", 
                           "filtered) and includes data from 18755 genes, 1601 ", 
                           "cell lines, 37 primary diseases and 33 lineages. "),
                    paste0("Metadata for cell lines in the 19Q1 DepMap release, ", 
                           "for 0 genes, 1677 cell lines, 38 primary diseases ", 
                           "and 33 lineages.")),
    BiocVersion = "3.10",
    Genome = "", 
    SourceType = "CSV", 
    SourceUrl = c(paste0("https://ndownloader.figshare.com/files/13515395"),
                  paste0("https://ndownloader.figshare.com/files/14221385"),
                  paste0("https://depmap.org/portal/download/api/download/external?file_name=ccle%2Fdepmap-wes-cn-data-97cc.14%2Fpublic_19Q1_gene_cn.csv"),
                  paste0("https://depmap.org/portal/download/api/download/external?file_name=ccle%2Fdepmap-rnaseq-expression-data-ccd0.12%2FCCLE_depMap_19Q1_TPM.csv"),
                  paste0("https://depmap.org/portal/download/api/download/external?file_name=ccle%2FCCLE_RPPA_20180123.csv"),
                  paste0("https://depmap.org/portal/download/api/download/external?file_name=ccle%2Fdepmap-mutation-calls-9a1a.7%2Fdepmap_19Q1_mutation_calls.csv"),
                  paste0("https://depmap.org/portal/download/api/download/external?file_name=processed_portal_downloads%2Fdepmap-public-cell-line-metadata-183e.4%2FDepMap-2019q1-celllines_v2.csv")),
    SourceVersion = "Feb 19 2019",
    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/rnai_19Q1.rda"), 
                  paste0("depmap/crispr_19Q1.rda"), 
                  paste0("depmap/copyNumber_19Q1.rda"), 
                  paste0("depmap/RPPA_19Q1.rda"), 
                  paste0("depmap/TPM_19Q1.rda"),
                  paste0("depmap/mutationCalls_19Q1.rda"),
                  paste0("depmap/metadata_19Q1.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 19Q1 release")

write.csv(meta_19Q1, file="../extdata/metadata_19Q1.csv", row.names=FALSE)
## to upload this metadata to EH, enter the following into the CL
## ExperimentHubData::makeExperimentHubMetadata("~/tmp/depmap/", fileName = "metadata_19Q2.csv")