Fix for chrBorders (function: split_genome) so it would work for both…

… non-numeric (e.g. "X") and numeric (e.g. 23) chromosome names
pblaney · Nov 17, 2021 · ae2425f · ae2425f
1 parent a484b64
commit ae2425f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/R/clonal_ascat.R b/R/clonal_ascat.R
@@ -7,7 +7,7 @@
 split_genome = function(SNPpos) {
   # look for gaps of more than 1Mb and chromosome borders
   holesOver1Mb = which(diff(SNPpos[,2])>=1000000)+1
-  chrBorders = which(diff(as.numeric(SNPpos[,1]))!=0)+1
+  chrBorders = which(diff(as.numeric(factor(SNPpos[,1],levels=unique(SNPpos[,1]))))!=0)+1
   holes = unique(sort(c(holesOver1Mb,chrBorders)))
 
   # find which segments are too small