inst/scripts/make-metadata.R

In Bishop-Laboratory/RLHub: An ExperimentHub package for accessing processed RLSuite data sets

#' Creates the metadata for RLHub

meta <- data.frame(
  Title = c(
    "Primary Genomic Annotations (hg38)",
    "Primary Genomic Annotations (mm10)",
    "Full Genomic Annotations (hg38)",
    "Full Genomic Annotations (mm10)",
    "R-loop Binding Proteins",
    "Gene Expression",
    "Feature Enrichment per Sample",
    "Feature Enrichment per RL-Region",
    "GS-Signal",
    "FFT-Model",
    "Feature-Prep Model",
    "RLFS-Test Results",
    "RLRegion Annotations",
    "RLRegion Metadata",
    "RLRegion Read Counts",
    "RLBase Sample Manifest"
  ),
  Description = c(
    paste0("Primary Human genomic annotations curated for use with RLSuite."),
    paste0("Primary Mouse genomic annotations curated for use with RLSuite."),
    paste0("Full Human genomic annotations curated for use with RLSuite."),
    paste0("Full Mouse genomic annotations curated for use with RLSuite."),
    paste0("R-loop-binding proteins discovered from mass-spec studies."),
    paste0("Gene expression count tables from matched RNA-Seq experiments ",
           "corresponding to R-loop profiling. The counts, TPM, and VST-",
           "transformed counts are provided."),
    paste0("Genomic feature enrichment stats for each peakset in RLBase."),
    paste0("Genomic feature enrichment stats for the RL-Regions in RLBase."),
    paste0("Bin-level read counts for RLBase samples around R-loop sites ",
           "discovered using long-read SMRF-Seq (gold-standard sites)."),
    paste0("Stacked classifier for deciding whether samples successfully mapped",
           " R-loops."),
    paste0("Model for transforming dataset features prior to classification."),
    paste0("The results from RLFS (R-loop-forming sequences) analysis on all",
           " RLBase samples via the RLSeq package."),
    paste0("R-loop regions (rlregions) derived from S9.6-based and dRNH-based",
           " samples ('All' group), annotated with genomic features."),
    paste0("R-loop regions (rlregions) derived from S9.6-based and dRNH-based",
           " samples ('All' group), with descriptive metadata."),
    paste0("Read count tables from RLBase samples quantified across the ",
           "R-loop regions (rlregions) derived from both S9.6-based and",
           " dRNH-based samples ('All' group)."),
    paste0("The hand-curated manifest of all RLBase samples ",
           "with descriptive metadata and some sample-level analysis results.")
  ),
  BiocVersion = "3.14",
  Genome = c(
    "hg38",
    "mm10",
    "hg38",
    "mm10",
    rep("hg38", 12)
  ),
  SourceType = c(
    rep("Multiple", 4),
    "XLS/XLSX",
    "FASTQ",
    rep("Multiple", 8), 
    "BAM", 
    "XLS/XLSX"
  ),
  SourceUrl = "https://github.com/Bishop-Laboratory/RLBase-data",
  SourceVersion = "v1",
  Species = c(
    "Homo sapiens",
    "Mus musculus",
    "Homo sapiens",
    "Mus musculus",
    rep("Homo sapiens", 12)
  ),
  TaxonomyId = c(
    9606,
    10090,
    9606,
    10090,
    rep(9606, 12)
  ),
  Coordinate_1_based = TRUE,
  DataProvider = "Multiple",
  Maintainer = "Henry Miller <millerh1@uthscsa.edu>",
  RDataClass = c(
    "list",
    "list",
    "list",
    "list",
    "tbl",
    "SummarizedExperiment",
    "tbl",
    "tbl",
    "tbl",
    "caretStack",
    "preProcess",
    "list",
    "tbl",
    "tbl",
    "SummarizedExperiment",
    "tbl"
  ),
  DispatchClass = "Rda",
  Location_Prefix = "https://rlbase-data.s3.amazonaws.com/",
  RDataPath = c(
    "RLHub/annotations_primary_hg38.rda",
    "RLHub/annotations_primary_mm10.rda",
    "RLHub/annotations_full_hg38.rda",
    "RLHub/annotations_full_mm10.rda",
    "RLHub/rlbps.rda",
    "RLHub/geneexp.rda",
    "RLHub/feature_enrichment_per_samples.rda",
    "RLHub/feature_enrichment_rlregions.rda",
    "RLHub/gsSignalRLBase.rda",
    "RLHub/fftModel.rda",
    "RLHub/prepFeatures.rda",
    "RLHub/rlfsres.rda",
    "RLHub/rlregions_annotations.rda",
    "RLHub/rlregions_table.rda",
    "RLHub/rlregions_counts.rda",
    "RLHub/rlsamples.rda"
  ),
  Tags = c(
    "annots_primary_hg38",
    "annots_primary_mm10",
    "annots_full_hg38",
    "annots_full_mm10",
    "rlbps",
    "gene_exp",
    "feat_enrich_samples",
    "feat_enrich_rlregions",
    "gs_signal",
    "fft_model",
    "prep_features",
    "rlfs_res",
    "rlregions_annot",
    "rlregions_meta",
    "rlregions_counts",
    "rlbase_samples"
  )
)

write.csv(meta, file="inst/extdata/metadata.csv", row.names=FALSE)