R/import_bigwig_filtered.R

In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

#' Import filtered bigwig
#'
#' Import a subset of a bigwig file
#' based on the coordinates in a \link[GenomicRanges]{GRanges} 
#' object (\code{gr.query_dat}).
#' @param bw.file Path to a bigwig file.
#' @param gr.query_dat \link[GenomicRanges]{GRanges}
#'  object to query the bigwig file with.
#' @param full_data Whether to return the actual read ranges
#'  (\code{full_data=TRUE}),
#' or just the "score" column which summarizes the height of
#' the aggregated reads across the genome (\code{full_data=TRUE}).
#' 
#' @keywords internal
#' @importFrom GenomicRanges mcols start end
#' @importFrom rtracklayer import.bw
import_bigwig_filtered <- function(bw.file,
                                   gr.query_dat,
                                   full_data = TRUE) {
    if (full_data) {
        #### Get all ranges within min/max ####
        gr.span <- gr.query_dat[1, ]
        GenomicRanges::mcols(gr.span) <- NULL
        GenomicRanges::start(gr.span) <-
            min(GenomicRanges::start(gr.query_dat), na.rm = TRUE)
        GenomicRanges::end(gr.span) <-
            max(GenomicRanges::end(gr.query_dat), na.rm = TRUE)
    } else {
        #### Otherwise, just use the score for the exact values ####
        gr.span <- gr.query_dat
    }
    # bw.dat <- rtracklayer::BigWigSelection(ranges = gr.query_dat,
    #                                        colnames = "score")
    bw.filt <- rtracklayer::import.bw(
        con = bw.file,
        selection = gr.span
    )
    # plot(x = start(bw.filt), y=bw.filt$score)
    return(bw.filt)
}