R/get_outfiles.R

In nearBynding: Discern RNA structure proximal to protein binding

#' @title get_outfiles
#'
#' @description Copy files necessary to complete the vignette onto the local
#' machine in cases where Stereogene, CapR, or bedtools are not available.
#'
#' @param dir Directory into which files ought to be stored. Default current
#' work directory.
#'
#' @return deposits six *.dist StereoGene output files into the selected
#' directory
#'
#' @examples
#' ## pull example StereoGene output files
#' get_outfiles()
#'
#' @export

get_outfiles <- function(dir = ".") {
    file.copy(system.file("extdata/stem_liftOver_chr4and5.dist",
        package = "nearBynding"), dir)
    file.rename(
        paste0(dir, "/stem_liftOver_chr4and5.dist"),
        paste0(dir, "/chr4and5_3UTR_stem_liftOver~chr4and5_liftOver.dist"))
    file.copy(system.file("extdata/bulge_liftOver_chr4and5.dist",
        package = "nearBynding"), dir)
    file.rename(
        paste0(dir, "/bulge_liftOver_chr4and5.dist"),
        paste0(dir, "/chr4and5_3UTR_bulge_liftOver~chr4and5_liftOver.dist"))
    file.copy(system.file("extdata/exterior_liftOver_chr4and5.dist",
        package = "nearBynding"), dir)
    file.rename(
        paste0(dir, "/exterior_liftOver_chr4and5.dist"),
        paste0(dir,"/chr4and5_3UTR_exterior_liftOver~chr4and5_liftOver.dist"))
    file.copy(system.file("extdata/internal_liftOver_chr4and5.dist",
        package = "nearBynding"), dir)
    file.rename(
        paste0(dir, "/internal_liftOver_chr4and5.dist"),
        paste0(dir,"/chr4and5_3UTR_internal_liftOver~chr4and5_liftOver.dist"))
    file.copy(system.file("extdata/hairpin_liftOver_chr4and5.dist",
        package = "nearBynding"), dir)
    file.rename(
        paste0(dir, "/hairpin_liftOver_chr4and5.dist"),
        paste0(dir,"/chr4and5_3UTR_hairpin_liftOver~chr4and5_liftOver.dist"))
    file.copy(system.file("extdata/multibranch_liftOver_chr4and5.dist",
        package = "nearBynding"), dir)
    file.rename(
        paste0(dir, "/multibranch_liftOver_chr4and5.dist"),
        paste0(dir,"/chr4and5_3UTR_multibranch_liftOver~chr4and5_liftOver.dist"
        ))
}