clean up

R/gt_helper_functions.R

@@ -10,23 +10,3 @@
 .gt_get_bigsnp<-function(.x){
   attr(.x$genotypes,"bigsnp")
 }
-
-
-# a developer function to create various count summaries of a population, used to
-# compute more complex statistics (e.g. pairwise fst, etc.).
-.gt_pop_freqs <- function(.x){
-  counts <- bigstatsr::big_counts( .gt_get_bigsnp(.x)$genotypes,
-                                   ind.row =.gt_bigsnp_rows(.x),
-                                   ind.col = .gt_bigsnp_cols(.x))
-  sums_alt <- apply(counts,2,function(x) x[2]+2*x[3])
-  n <- apply(counts,2,function(x) sum(x[1:3])*2)
-  sums_ref <- n - sums_alt
-  freq_alt <- sums_alt/n
-  freq_ref <- 1- freq_alt
-  het_obs <- apply(counts,2,function(x) x[2]/sum(x[1:3]))
-  return (list(
-    freq_alt = freq_alt,
-    freq_ref = freq_ref,
-    n = n,
-    het_obs = het_obs))
-}

R/gt_roh_window.R

@@ -42,8 +42,8 @@
 #' @export
 #'
 #' @examples
-#' # don't run the example
-#' if (FALSE) {
+#' # run the example only if we have the package installed
+#' if (requireNamespace("detectRUNS", quietly = TRUE)) {
 #' sheep_ped <- system.file("extdata", "Kijas2016_Sheep_subset.ped",
 #'     package="detectRUNS")
 #' sheep_gt <- tidypopgen::gen_tibble(sheep_ped, backingfile = tempfile(),