--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/stats/correlation.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,84 @@
+#!/usr/bin/perl
+
+###########################################################################
+# Purpose: To calculate the correlation of two sets of scores in one file.
+# Usage: correlation.pl infile.bed output.txt column1 column2
+#        (column start from 1)
+# Written by: Yi Zhang  (June, 2005)
+###########################################################################
+if (!$ARGV[0] || !$ARGV[1] || !defined($ARGV[2]) || !defined($ARGV[3]) ) {
+   print STDERR "Usage: correlation.pl infile.bed output.txt column1 column2\n";
+   print STDERR "       (column start from 1)\n"; 
+   exit;
+}
+my $file = $ARGV[0];
+my $out = $ARGV[1];
+
+die "<font color=\"yellow\">The input columns contain numerical values: $ARGV[2], $ARGV[3]</font>.\n" if ($ARGV[2] =~ /[a-zA-Z]+/ || $ARGV[3] =~ /[a-zA-Z]+/);
+
+my $col1 = $ARGV[2] - 1;
+my $col2 = $ARGV[3] - 1;
+
+my ($f, $o);
+my (@a, @b);
+
+my $n_t = 0;
+open($f, $file) or die "Could't open $file, $!\n";
+while(<$f>) {
+  chomp;
+  my @t = split(/\t/);
+  if ($n_t == 0) { 
+     $n_t = scalar(@t) - 1; 
+     die "<font color=\"yellow\">The input column number exceeds the size of the file: $col1, $col2, $n_t</font>\n" if ( $col1 > $n_t || $col2 > $n_t );
+  }
+  die "<font color=\"yellow\">The columns you have selected contain non numeric characters:$t[$col1] and $t[$col2] \n</font>" if ($t[$col1] =~ /[a-zA-Z]+/ || $t[$col2] =~ /[a-zA-Z]+/);  
+  push(@a, $t[$col1]);
+  push(@b, $t[$col2]);
+}
+close($f);
+
+my $result = correlation(\@a, \@b);
+
+open($o, ">$out") or die "Couldn't open $out, $!\n";
+$col1 = $col1 + 1;
+$col2 = $col2 + 1;
+print $o "The correlation of column $col1 and $col2 is $result\n";
+close($o);
+print "The correlation of column $col1 and $col2 is $result\n";
+
+sub correlation {
+   my ($array1ref, $array2ref) = @_;
+   my ($sum1, $sum2);
+   my ($sum1_squared, $sum2_squared); 
+   foreach (@$array1ref) { $sum1 += $_;  $sum1_squared += $_**2; }
+   foreach (@$array2ref) { $sum2 += $_;  $sum2_squared += $_**2; }
+   my $numerator = (@$array1ref**2) * covariance($array1ref, $array2ref);
+   my $denominator = sqrt(((@$array1ref * $sum1_squared) - ($sum1**2)) *
+                          ((@$array1ref * $sum2_squared) - ($sum2**2)));
+   my $r;
+   if ($denominator == 0) {
+     print STDERR "The denominator is 0.\n";
+	 exit 0; 
+   } else {
+      $r = $numerator / $denominator;
+   }
+    return $r;
+}
+
+sub covariance {
+   my ($array1ref, $array2ref) = @_;
+   my ($i, $result);
+   for ($i = 0; $i < @$array1ref; $i++) {
+       $result += $array1ref->[$i] * $array2ref->[$i];
+   }
+   $result /= @$array1ref;
+   $result -= mean($array1ref) * mean($array2ref);
+}
+
+sub mean {
+  my ($arrayref) = @_;
+  my $result;
+  foreach (@$arrayref) { $result += $_; }
+  return $result/@$arrayref;
+}
+