add chr_step, length2total

seq/chr_lengths.r

@@ -1,4 +1,5 @@
 .genome = import('./genome')$genome
+`%>%` = magrittr::`%>%`
 
 #' Get chromosome lengths from assembly ID
 #'
@@ -22,3 +23,35 @@ chr_lengths.default = function(assembly, chrs=NULL) {
     chr_lengths = GenomeInfoDb::seqlengths(assembly)
     chr_lengths[names(chr_lengths) %in% chrs]
 }
+
+#' Generate stepwise data points along chromosomes
+#'
+#' @param step  Step size in bases (default: 1e7)
+#' @param assembly  Which assembly to use (default: GRCh38)
+#' @param chrs  Chromosomes to include (default: 1:22,X)
+#' @param min_n  Minimum number of data points per chromosome
+#' @return  data.frame with fields: chr, length, steps [list of numeric]
+chr_step = function(step=1e7, assembly="GRCh38", chrs=NULL, min_n=7) {
+    chr_lengths(assembly=assembly, chrs=chrs) %>%
+        stack() %>%
+        dplyr::select(chr=ind, length=values) %>%
+        dplyr::rowwise() %>%
+        dplyr::mutate(steps = list(seq(1, length, length.out=max(min_n, round(length/step))))) %>%
+        dplyr::select(-length)
+}
+
+#' Convert chromosome positions to total positions
+#'
+#' @param chr  Vector of chromosomes
+#' @param pos  Vector of chromosome positions
+#' @return     Numeric vector with absolute chromosome positions
+chr2total_pos = function(chr, pos) {
+    old = data.frame(chr=chr, pos=pos)
+    add = chr_lengths() %>%
+        dplyr::transmute(chr = chr,
+                         add_len = c(0, cumsum(as.numeric(length))[-nrow(.)]))
+
+    dplyr::left_join(old, add, by="chr") %>%
+        dplyr::mutate(pos = pos + add_len) %>%
+        dplyr::pull(pos)
+}