#!/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 "The input columns contain numerical values: $ARGV[2], $ARGV[3].\n" if ($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 "The input column number exceeds the size of the file: $col1, $col2, $n_t\n" if ( $col1 > $n_t || $col2 > $n_t );
}
die "The columns you have selected contain non numeric characters:$t[$col1] and $t[$col2] \n" 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;
}