R/read_encode_cgi.R

In andreaskapou/BPRMeth-devel: Model higher-order methylation profiles

#' Read file containing CpG island locations
#'
#' \code{read_encode_cgi} reads a file containing CpG island (CGI) locations in
#' the human genome using the \code{\link[data.table]{fread}} function.
#'
#' @inheritParams read_bs_encode_haib
#'
#' @return A \code{\link[GenomicRanges]{GRanges}} object if \code{is_GRanges} is
#'   TRUE, otherwise a \code{\link[data.table]{data.table}} object.
#'
#'   The GRanges object contains one additional metadata column: \itemize{ \item
#'   \code{cgi_id}: Unique ID of the CpG Island. } This column can be accessed
#'   as follows: \code{granges_object$id}
#'
#' @author C.A.Kapourani \email{C.A.Kapourani@@ed.ac.uk}
#'
#' @seealso \code{\link{read_rna_encode_caltech}},
#'   \code{\link{read_bs_encode_haib}}
#'
#' @examples
#' \dontrun{
#' # Download the file and change the working directory to that location
#' file <- "name_of_CGI_file")
#' cgi_data <- read_encode_cgi(file)
#'
#' # Extract the CGI ID
#' cgi_id <- cgi_data$id
#' }
#'
#' @export
read_encode_cgi <- function(file, is_GRanges = TRUE){
    message("Reading file ", file, " ...")
    cgi_data <- data.table::fread(input = file,
                              sep = "\t",
                              header = FALSE,
                              col.names = c("chr", "start", "end", "id"))

    N <- NROW(cgi_data)
    cgi_data$id <- paste0("cgi_", seq(1, N))

    if (is_GRanges){
        # Create a GRanges object -----------------------------------
        message("Creating GRanges object ...")
        cgi_data <- GenomicRanges::GRanges(seqnames = cgi_data$chr,
                           ranges = IRanges::IRanges(start = cgi_data$start,
                                                     end   = cgi_data$end),
                           id = cgi_data$id)
    }
    message("Finished reading CGI file!\n")
    return(cgi_data)
}