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comparison tools/stats/correlation.pl @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/perl
2
3 ###########################################################################
4 # Purpose: To calculate the correlation of two sets of scores in one file.
5 # Usage: correlation.pl infile.bed output.txt column1 column2
6 # (column start from 1)
7 # Written by: Yi Zhang (June, 2005)
8 ###########################################################################
9 if (!$ARGV[0] || !$ARGV[1] || !defined($ARGV[2]) || !defined($ARGV[3]) ) {
10 print STDERR "Usage: correlation.pl infile.bed output.txt column1 column2\n";
11 print STDERR " (column start from 1)\n";
12 exit;
13 }
14 my $file = $ARGV[0];
15 my $out = $ARGV[1];
16
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]+/);
18
19 my $col1 = $ARGV[2] - 1;
20 my $col2 = $ARGV[3] - 1;
21
22 my ($f, $o);
23 my (@a, @b);
24
25 my $n_t = 0;
26 open($f, $file) or die "Could't open $file, $!\n";
27 while(<$f>) {
28 chomp;
29 my @t = split(/\t/);
30 if ($n_t == 0) {
31 $n_t = scalar(@t) - 1;
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 > $n_t );
33 }
34 die "<font color=\"yellow\">The columns you have selected contain non numeric characters:$t[$col1] and $t[$col2] \n</font>" if ($t[$col1] =~ /[a-zA-Z]+/ || $t[$col2] =~ /[a-zA-Z]+/);
35 push(@a, $t[$col1]);
36 push(@b, $t[$col2]);
37 }
38 close($f);
39
40 my $result = correlation(\@a, \@b);
41
42 open($o, ">$out") or die "Couldn't open $out, $!\n";
43 $col1 = $col1 + 1;
44 $col2 = $col2 + 1;
45 print $o "The correlation of column $col1 and $col2 is $result\n";
46 close($o);
47 print "The correlation of column $col1 and $col2 is $result\n";
48
49 sub correlation {
50 my ($array1ref, $array2ref) = @_;
51 my ($sum1, $sum2);
52 my ($sum1_squared, $sum2_squared);
53 foreach (@$array1ref) { $sum1 += $_; $sum1_squared += $_**2; }
54 foreach (@$array2ref) { $sum2 += $_; $sum2_squared += $_**2; }
55 my $numerator = (@$array1ref**2) * covariance($array1ref, $array2ref);
56 my $denominator = sqrt(((@$array1ref * $sum1_squared) - ($sum1**2)) *
57 ((@$array1ref * $sum2_squared) - ($sum2**2)));
58 my $r;
59 if ($denominator == 0) {
60 print STDERR "The denominator is 0.\n";
61 exit 0;
62 } else {
63 $r = $numerator / $denominator;
64 }
65 return $r;
66 }
67
68 sub covariance {
69 my ($array1ref, $array2ref) = @_;
70 my ($i, $result);
71 for ($i = 0; $i < @$array1ref; $i++) {
72 $result += $array1ref->[$i] * $array2ref->[$i];
73 }
74 $result /= @$array1ref;
75 $result -= mean($array1ref) * mean($array2ref);
76 }
77
78 sub mean {
79 my ($arrayref) = @_;
80 my $result;
81 foreach (@$arrayref) { $result += $_; }
82 return $result/@$arrayref;
83 }
84