New function, bin_splitter

R/bin_splitter.R

@@ -0,0 +1,65 @@
+#' @title Bin Splitter
+#' 
+#' @description This function takes a region and splits it into bins of a 
+#' specified size.
+#' 
+#' @details This function internally calls the purify_regions function to 
+#' properly format the incoming regions.Thus, thuis function can accept either a 
+#' data frame of regions or individual region coordinates.
+#'
+#' @param these_regions The region(s) to be queried. Can be a data frame with
+#' regions with the following columns; chrom, start, end.
+#' Or in a string in the following format chr:start-end.
+#' @param qchrom Query chromosome (prefixed or un-prefixed),
+#' Required if `these_regions` is not provided.
+#' @param qstart Query start position. Required if `these_regions` is not provided.
+#' @param qend Query end position. Required if `these_regions` is not provided.
+#' @param bin_size The size of the bins to split the regions into, default is 1000.
+#'
+#' @return A data frame with input regions binned into the specified bin size.
+#' 
+#' @import dplyr
+#' 
+#' @export
+#'
+#' @examples
+#' #Example 1 - Call function with regions specified individually
+#' my_bins = bin_splitter(qchrom = c("chr1", "chr2"), 
+#'                        qstart = c(100, 200), 
+#'                        qend = c(200, 300),
+#'                        bin_size = 10)
+#'
+#' #Example 2 - Call the funciton with regions from a data frame
+#' my_regions = purify_regions(these_regions = c("chr7:1000-500000", "chr8:50000-7000000"))
+#' these_bins = bin_splitter(these_regions = my_regions, bin_size = 100000)
+#' 
+bin_splitter = function(these_regions = NULL, 
+                        qchrom = NULL,
+                        qstart = NULL,
+                        qend = NULL,
+                        bin_size = 1000){
+
+  #call helperto format regions
+  my_regions = purify_regions(these_regions = these_regions,
+                              qchrom = qchrom,
+                              qstart = qstart,
+                              qend = qend)
+
+  bin_region = function(my_regions, 
+                        bin_size){
+
+    bin_df = data.frame(bin_chr = my_regions$chrom, 
+                        bin_start = seq(my_regions$start, my_regions$end, bin_size))
+
+    bin_df = mutate(bin_df, bin_end = bin_start + bin_size) %>%
+      dplyr::filter(bin_end <= my_regions$end)
+
+    return(bin_df)
+  }
+
+  #call helper to bin the regions
+  binned_regions = lapply(1:nrow(my_regions), function(i) bin_region(my_regions[i,], bin_size))
+  binned_regions = do.call(rbind, binned_regions)
+
+  return(binned_regions)
+}