inst/scripts/make-metadata.R

In databio/GenomicDistributionsData: Reference data for GenomicDistributions package

### =========================================================================
### GenomicDistributions Metadata
### -------------------------------------------------------------------------
###


GD = "GenomicDistributionsData/data/"
meta <- data.frame(
  Title = c("chromSizes_hg19", "chromSizes_hg38", "chromSizes_mm9", "chromSizes_mm10",
            "TSS_hg19", "TSS_hg38", "TSS_mm9", "TSS_mm10",
            "geneModels_hg19", "geneModels_hg38", "geneModels_mm9", "geneModels_mm10",
            "openSignalMatrix_hg19", "openSignalMatrix_hg38", "openSignalMatrix_mm10"),
  Description = c("A dataset containing chromosome sizes for the Homo sapiens hg19 genome assembly",
                  "A dataset containing chromosome sizes for the Homo sapiens hg38 genome assembly",
                  "A dataset containing chromosome sizes for the Mus musculus mm9 genome assembly",
                  "A dataset containing chromosome sizes for the Mus musculus mm10 genome assembly",
                  "A dataset containing Transcription Start Sites (TSS) for the Homo sapiens hg19 genome assembly",
                  "A dataset containing Transcription Start Sites (TSS) for the Homo sapiens hg38 genome assembly",
                  "A dataset containing Transcription Start Sites (TSS) for the Mus musculus mm9 genome assembly",
                  "A dataset containing Transcription Start Sites (TSS) for the Mus musculus mm10 genome assembly",
                  "A dataset containing gene and exons locations for the Homo sapiens hg19 genome assembly",
                  "A dataset containing gene and exons locations for the Homo sapiens hg38 genome assembly",
                  "A dataset containing gene and exons locations for the Mus musculus  mm9 genome assembly",
                  "A dataset containing gene and exons locations for the Mus musculus  mm10 genome assembly",
                  "A dataset containing open chromatin regions across all cell types defined by ENCODE for Homo sapiens hg19",
                  "A dataset containing open chromatin regions across all cell types defined by ENCODE for Homo sapiens hg38",
                  "A dataset containing open chromatin regions across all cell types defined by ENCODE for Mus musculus mm10"),
  BiocVersion = rep("3.12", 15),
  Genome = c(rep(c("hg19", "hg38", "mm9", "mm10"), 3), "hg19", "hg38", "mm10"), 
  SourceType = c(rep("UCSC track", 4), rep(c("ensembl", "ensembl", "ensembl", "ensembl"), 2), rep("TXT", 3)), 
  SourceUrl = c("https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html",
                "https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html",
                "https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Mmusculus.UCSC.mm9.html",
                "https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Mmusculus.UCSC.mm10.html",
                "https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v75.html",
                "https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v86.html",
                "https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Mmusculus.v79.html",
                "https://bioconductor.org/packages/release/data/annotation/html/TxDb.Mmusculus.UCSC.mm9.knownGene.html",
                "https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v75.html",
                "https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v86.html",
                "https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Mmusculus.v79.html",
                "https://bioconductor.org/packages/release/data/annotation/html/TxDb.Mmusculus.UCSC.mm9.knownGene.html",
                "http://big.databio.org/open_chromatin_matrix/openSignalMatrix_hg19_percentile99_01_quantNormalized_round4d.txt.gz",
                "http://big.databio.org/open_chromatin_matrix/openSignalMatrix_hg38_percentile99_01_quantNormalized_round4d.txt.gz",
                "http://big.databio.org/open_chromatin_matrix/openSignalMatrix_mm10_percentile99_01_quantNormalized_round4d.txt.gz"),
  SourceVersion = "Sep 2 2020",
  Species = c(rep(c("Homo sapiens", "Homo sapiens", "Mus musculus", "Mus musculus"), 3), rep("Homo sapiens", 2), "Mus musculus"),
  TaxonomyId = c(rep(c(9606, 9606, 10090, 10090), 3), rep(9606, 2), 10090),
  Coordinate_1_based = TRUE,
  DataProvider = "Ensdb",
  Maintainer = "Michal Stolarczyk <mjs5kd@virginia.edu>",
  RDataClass = c(rep("Int", 4), rep("GRanges", 4), rep("list with 4 GRanges", 4), rep("data.table", 3)) ,
  DispatchClass = c(rep("Rda", 15)),
  RDataPath = c(paste0(GD, "chromSizes_hg19.rda"),
                paste0(GD, "chromSizes_hg38.rda"),
                paste0(GD, "chromSizes_mm9.rda"),
                paste0(GD, "chromSizes_mm10.rda"),
                paste0(GD, "TSS_hg19.rda"),
                paste0(GD, "TSS_hg38.rda"),
                paste0(GD, "TSS_mm9.rda"),
                paste0(GD, "TSS_mm10.rda"),
                paste0(GD, "geneModels_hg19.rda"),
                paste0(GD, "geneModels_hg38.rda"),
                paste0(GD, "geneModels_mm9.rda"),
                paste0(GD, "geneModels_mm10.rda"),
                paste0(GD, "openSignalMatrix_hg19.rda"),
                paste0(GD, "openSignalMatrix_hg38.rda"), 
                paste0(GD, "openSignalMatrix_mm10.rda")),
  Tags = ""
)

write.csv(meta, file="inst/extdata/metadata.csv", row.names=FALSE)
#ExperimentHubData::makeExperimentHubMetadata("~/Desktop/GDdata_release/GenomicDistributionsData", fileName = "metadata.csv")