[Seqinr-commits] r1737 - pkg/R

[noreply at r-forge.r-project.org]

Author: lobry
Date: 2010-03-07 12:12:45 +0100 (Sun, 07 Mar 2010)
New Revision: 1737

Added:
   pkg/R/rho.R
Log:
rho() has gained a wordsize argument as suggested by Avril Coghlan

Added: pkg/R/rho.R
===================================================================
--- pkg/R/rho.R	                        (rev 0)
+++ pkg/R/rho.R	2010-03-07 11:12:45 UTC (rev 1737)
@@ -0,0 +1,16 @@
+rho <- function (sequence, wordsize = 2, alphabet = s2c("acgt"))
+{
+  wordcount <- count(sequence, wordsize, freq = FALSE, alphabet = alphabet)
+  uni <- count(sequence, 1, freq = TRUE, alphabet = alphabet)
+
+  expected_wordfreq <- function (wordsize, uni) 
+  {
+    if (wordsize == 1) 
+        return(uni)
+    else kronecker(uni, expected_wordfreq(wordsize - 1, uni))
+  }
+
+  expected_wordcount <- sum(wordcount)*expected_wordfreq(wordsize, uni)
+   
+  return(wordcount/expected_wordcount)
+}