Thresholds changed

imgag · Dec 5, 2019 · 9789c18 · 9789c18
1 parent 61d3d77
commit 9789c18
Showing 1 changed file with 9 additions and 1 deletion.
diff --git a/generalHelpers.R b/generalHelpers.R
@@ -120,8 +120,16 @@ gc_and_sample_size_normalise <- function(info, coverages, averageCoverage=T, all
   gcs <- info[,4]
   uniques_gcs <- unique(gcs)
   uniquesGcsToExclude = c()
+  empricial_criterion_for_exclusion = 25
+  if (nrow(coverages) > 10000) {
+    empricial_criterion_for_exclusion = 50
+  }
+  if (nrow(coverages) > 100000) {
+    empricial_criterion_for_exclusion = 100
+  }
+
   for (i in 1:length(uniques_gcs)) {
-    if (length(which(gcs == uniques_gcs[i])) < 25) {
+    if (length(which(gcs == uniques_gcs[i])) < empricial_criterion_for_exclusion) {
       uniquesGcsToExclude = c(uniquesGcsToExclude, i)
     }
   }