R/bedToGRangesList.R

In stilianoudakis/preciseTAD: preciseTAD: A machine learning framework for precise TAD boundary prediction

#' Function to create a GRangesList object from functional genomic annotation
#' data in the form of BED files
#'
#' @param filepath Character describing the path to the folder containing the
#' BED files of functional genomic annotations. This is ignored if bedList is
#' specified.
#' @param bedList A list object containing the bed data as data frames to be
#' converted into a GRangesList. The data frames must include at least
#' chromosome, start, and end coordinates as the first 3 columns. Default is
#' NULL.
#' @param bedNames A character vector to provide names to the GRangesList,
#' should be in the order of bedList. Default is NULL.
#' @param pattern Character describing the pattern of the files for the
#' functional genomic annotations. Default is "*.bed".
#' @param signal The column number in the BED files that denotes coverage 
#' strength. Must be the same for all files. Default is NULL indicating to no 
#' coverage value is to be used.
#'
#' @return A \code{GRangesList} object where each entry is a \code{GRanges}
#' object specific to each BED file in the path provided
#' @export
#'
#' @importFrom utils read.table
#' @import IRanges GenomicRanges
#'
#' @examples
#' #set path
#' path <- system.file("extdata", package = "preciseTAD")
#' #contains 2 BED files representing YY1 and NFYA
#' #transcription factor binding sites for GM12878
#' tfbsList <- bedToGRangesList(filepath = path, bedList=NULL, bedNames=NULL,
#' pattern = "*.bed", signal=NULL)
bedToGRangesList <- function(filepath, bedList=NULL, bedNames=NULL, 
                             pattern = "*.bed", signal = NULL) {

    #CREATING GRangesList#

    annots_gr_list <- GRangesList()
    # if(grepl(paste0(names, collapse = '|'), list.files(filepath)))

    if(is.null(bedList)) {
        for (i in seq_len(length(list.files(filepath, pattern = pattern)))) {
            dat <- read.table(paste0(filepath, "/", list.files(filepath, pattern = pattern)[i]),
                              header = FALSE)

            annots_gr_list[[i]] <- GRanges(seqnames = dat$V1, IRanges(start = dat$V2,
                                                                      end = dat$V3))

            if (!(is.null(signal))) {
                mcols(annots_gr_list[[i]])$coverage <- dat[, signal]
            }

        }

        names(annots_gr_list) <- gsub(pattern, "", list.files(filepath, pattern = pattern))

    } else {
        for(i in seq_len(length(bedList))) {
            annots_gr_list[[i]] <- GRanges(seqnames = bedList[[i]][,1],
                                           IRanges(start = bedList[[i]][,2],
                                                   end = bedList[[i]][,3]))

            if (!(is.null(signal))) {
                mcols(annots_gr_list[[i]])$coverage <- bedList[[i]][,signal]
            }
        }

        names(annots_gr_list) <- bedNames
    }

    return(annots_gr_list)
}