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1 #!/usr/bin/perl
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2
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3 ###########################################################################
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4 # Purpose: To calculate the correlation of two sets of scores in one file.
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5 # Usage: correlation.pl infile.bed output.txt column1 column2
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6 # (column start from 1)
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7 # Written by: Yi Zhang (June, 2005)
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8 ###########################################################################
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9 if (!$ARGV[0] || !$ARGV[1] || !defined($ARGV[2]) || !defined($ARGV[3]) ) {
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10 print STDERR "Usage: correlation.pl infile.bed output.txt column1 column2\n";
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11 print STDERR " (column start from 1)\n";
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12 exit;
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13 }
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14 my $file = $ARGV[0];
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15 my $out = $ARGV[1];
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16
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17 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]+/);
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18
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19 my $col1 = $ARGV[2] - 1;
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20 my $col2 = $ARGV[3] - 1;
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21
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22 my ($f, $o);
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23 my (@a, @b);
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24
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25 my $n_t = 0;
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26 open($f, $file) or die "Could't open $file, $!\n";
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27 while(<$f>) {
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28 chomp;
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29 my @t = split(/\t/);
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30 if ($n_t == 0) {
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31 $n_t = scalar(@t) - 1;
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32 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 > $n_t );
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33 }
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34 die "<font color=\"yellow\">The columns you have selected contain non numeric characters:$t[$col1] and $t[$col2] \n</font>" if ($t[$col1] =~ /[a-zA-Z]+/ || $t[$col2] =~ /[a-zA-Z]+/);
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35 push(@a, $t[$col1]);
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36 push(@b, $t[$col2]);
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37 }
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38 close($f);
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39
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40 my $result = correlation(\@a, \@b);
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41
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42 open($o, ">$out") or die "Couldn't open $out, $!\n";
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43 $col1 = $col1 + 1;
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44 $col2 = $col2 + 1;
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45 print $o "The correlation of column $col1 and $col2 is $result\n";
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46 close($o);
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47 print "The correlation of column $col1 and $col2 is $result\n";
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48
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49 sub correlation {
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50 my ($array1ref, $array2ref) = @_;
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51 my ($sum1, $sum2);
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52 my ($sum1_squared, $sum2_squared);
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53 foreach (@$array1ref) { $sum1 += $_; $sum1_squared += $_**2; }
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54 foreach (@$array2ref) { $sum2 += $_; $sum2_squared += $_**2; }
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55 my $numerator = (@$array1ref**2) * covariance($array1ref, $array2ref);
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56 my $denominator = sqrt(((@$array1ref * $sum1_squared) - ($sum1**2)) *
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57 ((@$array1ref * $sum2_squared) - ($sum2**2)));
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58 my $r;
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59 if ($denominator == 0) {
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60 print STDERR "The denominator is 0.\n";
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61 exit 0;
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62 } else {
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63 $r = $numerator / $denominator;
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64 }
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65 return $r;
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66 }
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67
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68 sub covariance {
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69 my ($array1ref, $array2ref) = @_;
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70 my ($i, $result);
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71 for ($i = 0; $i < @$array1ref; $i++) {
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72 $result += $array1ref->[$i] * $array2ref->[$i];
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73 }
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74 $result /= @$array1ref;
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75 $result -= mean($array1ref) * mean($array2ref);
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76 }
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77
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78 sub mean {
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79 my ($arrayref) = @_;
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80 my $result;
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81 foreach (@$arrayref) { $result += $_; }
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82 return $result/@$arrayref;
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83 }
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84
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