bugfixes

RPR-Genetic_code_optimality.R

@@ -3,12 +3,13 @@
 # Purpose:  A Bioinformatics Course:
 #              R code accompanying the RPR-Genetic_code_optimality unit.
 #
-# Version:  1.0
+# Version:  1.0.1
 #
 # Date:     2017  10  16
 # Author:   Boris Steipe (boris.steipe@utoronto.ca)
 #
 # Versions:
+#           1.0.1    Fixed two bugs discovered by Suan Chin Yeo.
 #           1.0      New material.
 #
 #
@@ -119,7 +120,7 @@ swappedGC <- function(GC) {
   #                       amino acids have been swapped.
 
   aaOrig <- unique(GC)                       # the amino acids in the input code
-  aaSwap <- sample(aa, length(aa))    # shuffled
+  aaSwap <- sample(aaOrig, length(aaOrig))   # shuffled
   names(aaSwap) <- aaOrig                    # name them after the original
   GC[1:64] <- aaSwap[GC]                     # replace original with shuffled
 
@@ -291,7 +292,7 @@ hist(valUGC,
 
 # This looks like a normal distribution. Let's assume the effect of mutations
 # under the universal genetic code is the mean of this distribution:
-effectUGC <- mean(val)  # 178.1
+effectUGC <- mean(valUGC)  # 178.1
 
 # Now we can look at the effects of alternate genetic codes: