R/extractSampleData.R

In graumannlab/readat: Functionality to Read and Manipulate SomaLogic ADAT files

#' Extract the sample datasets
#'
#' Extracts the sample datasets from the ZIP files in the \code{extdata}
#' directory.
#' @param somascanMenuVersion String describing which data file to extract.
#' Either "1.3k" or "1.1k".
#' @param intermediateDir A path to a directory to extract the ADATY file into.
#' @return A path to the extracted ADAT file.
#' @examples
#' extractSampleData() ##1.3k dataset by default
#' extractSampleData("1.1k")
#' @importFrom utils unzip
#' @export
extractSampleData <- function(somascanMenuVersion = c("1.3k", "1.1k"),
    intermediateDir = tempdir())
{
    somascanMenuVersion <- match.arg(somascanMenuVersion)
    if(!file.exists(intermediateDir))
    {
        dir.create(intermediateDir, recursive = TRUE)
    }
    zipFile <- system.file(
        "extdata",
        paste("PLASMA", somascanMenuVersion, "20151030.adat.zip", sep = "."),
        package = "readat"
    )
    unzip(zipFile, exdir = intermediateDir)
    file.path(
        intermediateDir,
        paste(
            "PLASMA",
            somascanMenuVersion,
            "HybNorm.MedNorm.Cal.20151030.adat",
            sep = "."
        )
    )
}