R/runStereogeneOnCapR.R

In vbusa1/nearBynding: Discern RNA structure proximal to protein binding

#' @title runStereogeneOnCapR
#'
#' @description Writes a configuration file and Stereogene script and runs
#' Stereogene for all CapR tracks
#'
#' @param dir_CapR_bg Directory of lifted-over CapR bedGraph files. Default
#' current directory
#' @param input_prefix Prefix string appended to input files; same as
#' input_prefix argument in processCapRout. Required
#' @param protein_file Name of protein file in bedGraph format. Required
#' @param output_prefix Prefix string to be appended to all output files.
#' Default to be same as input_prefix
#' @param chrom_size Name of chromosome size file. File must be in two-column
#' format without a header where first column is chromosome name and second
#' column is chromosome length, as from getChainChrSize. Required
#' @param name_config Name of output config file. Default config.cfg
#' @param nShuffle Number of permutations used to estimate error. Default 100.
#' @param get_error Whether to calculate the standard error of background
#' permutations from nShuffle. FALSE will save calculation time. Default FALSE
#' @param ... includes all other parameters acceptable to write_config and
#' write_stereogene
#'
#' @return generates StereoGene output files, including *.dist files
#'
#' @examples
#' runStereogeneOnCapR(protein_file = "chr4and5_liftOver.bedGraph",
#'                    chrom_size = "chr4and5_3UTR.size",
#'                    name_config = "chr4and5_3UTR.cfg",
#'                    input_prefix = "chr4and5_3UTR")
#'
#' @importFrom R.utils doCall
#'
#' @export

runStereogeneOnCapR <- function(dir_CapR_bg = ".",
                                input_prefix,
                                protein_file,
                                output_prefix = input_prefix,
                                name_config = "config.cfg",
                                chrom_size,
                                nShuffle = 100,
                                get_error = FALSE,
                                ...) {
    if (missing(chrom_size)){stop("please provide a chrom_size file")}
    doCall(write_config, args = list(...,
                                    name_config = name_config,
                                    chrom_size = chrom_size))
    for(context in c("hairpin", "stem", "multibranch",
                     "exterior", "internal", "bulge")){
        track_files <- c(paste0(dir_CapR_bg, "/", input_prefix, "_",
                                context, "_liftOver.bedGraph"), protein_file)
        name_sh <- paste0(output_prefix, "_stereogene_", context, ".sh")
        doCall(runStereogene, args = list(...,
                                          track_files = track_files,
                                          name_sh = name_sh,
                                          name_config = name_config,
                                          nShuffle = nShuffle,
                                          get_error = get_error))
    }
}