R/local_metadata.R

In LieberInstitute/GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode

#' Locate local metadata outside of AnnotationHub
#'
#' @param local_path A `character(1)` pointing to where the data is stored
#' locally
#'
#' @return The AnnotationHub metadata `data.frame()` for the data in this
#' package with `RDataPath` updated to point to the `local_path`. It includes
#' an addtional column called `loadCode` which you can evaluate with
#' `eval(parse(text = entry))`.
#'
#' @author Leonardo Collado-Torres
#' @seealso [AnnotationHubData::makeAnnotationHubMetadata()]
#' @export
#'
#' @examples
#'
#' ## Get the local metadata
#' meta <- local_metadata()
#'
#' ## Subset to the data of interest, lets say hg19 TxDb for v31
#' interest <- subset(meta, RDataClass == "TxDb" & Tags == "Gencode:v31:hg19")
#'
#' ## Inspect the result
#' interest
#'
#' ## Next you can load the data
#' if (file.exists(interest$RDataPath)) {
#'     ## This only works at JHPCE
#'     eval(parse(text = interest$loadCode))
#'
#'     ## Explore the loaded object (would be gencode_v31_hg19_txdb in this case)
#'     gencode_v31_hg19_txdb
#' }
local_metadata <- function(
        local_path = "/dcl01/lieber/ajaffe/lab/GenomicState/data-raw") {
    ## Locate and read AnnotationHub csv files
    csv_files <- dir(system.file("extdata", package = "GenomicState"),
        pattern = "^metadata.*\\.csv$", full.names = TRUE
    )
    meta <- do.call(rbind, lapply(csv_files, utils::read.csv,
        stringsAsFactors = FALSE,
        row.names = NULL
    ))

    ## Replace the RDataPath
    meta$RDataPath <- file.path(local_path, gsub(
        "GenomicState/", "",
        meta$RDataPath
    ))

    meta$loadCode <- paste0(
        gsub("\\.rda|\\.sqlite", "", basename(meta$RDataPath)),
        " <- ",
        ifelse(meta$DispatchClass == "SQLiteFile", "AnnotationDbi::loadDb",
            "load"
        ),
        '("',
        meta$RDataPath,
        '")'
    )

    return(meta)
}