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R/utils.R

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+#' Match bed-like entries to Hi-C bin indices
+#'
+#' @inheritParams PESCAn
+#' @param mode A \code{character} of length 1 indicating what position of the
+#'   \code{bed} argument to match with the indices. Possible values:
+#'   \code{"center"}, \code{"start"} or \code{"end"}.
+#'
+#' @return An \code{integer} vector of length \code{nrow(bed)} and parallel to
+#'   \code{bed} with indices to the Hi-C matrix.
+#'
+#' @details Out of bounds values are matched to nearest bin.
+#' @export
+bed2idx <- function(ABS, bed, mode = c("centre", "start", "end")) {
+  # American/British spelling
+  mode <- gsub("center", "centre", mode)
+  mode <- match.arg(mode, c("centre", "start", "end"))
+
+  # Reformat bed depending on mode
+  bed <- cbind.data.frame(
+    V1 = bed[, 1],
+    V2 = switch(mode,
+      "centre" = (bed[, 2] + bed[, 3]) / 2,
+      "start" = bed[, 2],
+      "end" = bed[, 3]
+    )
+  )
+
+  # Assign entries to shared chromosomes
+  chroms <- intersect(ABS[, 1], bed[, 1])
+  bed_group <- match(bed[, 1], chroms)
+  ABS_group <- match(ABS[, 1], chroms)
+
+  # Split by chromosome
+  bed_chrom <- split(bed[, 2], bed_group)
+  ABS_chrom <- split(ABS[, c(2, 4)], ABS_group)
+
+  # Match bed entry to idx
+  out <- mapply(function(i, j) {
+    j[pmax(findInterval(i, j[, 1]), 1), 2]
+  }, i = bed_chrom, j = ABS_chrom)
+  unsplit(out, bed_group)
+}
+
+
+# taken from ggplot
+try_require <- function(package, fun, source = NULL) {
+  if (requireNamespace(package, quietly = TRUE)) {
+    return(invisible())
+  }
+
+  if(source == 'BIOC'){
+    stop("Package `", package, "` required for `", fun , "`.\n",
+         "Please install from Bioconductor and try again.", call. = FALSE)
+  } else   if(source == 'github'){
+    stop("Package `", package, "` required for `", fun , "`.\n",
+         "Please install from github and try again.", call. = FALSE)
+  } else {
+    stop("Package `", package, "` required for `", fun , "`.\n",
+         "Please install and try again.", call. = FALSE)
+  }
+
+}