use R;

# This tests the AUTOLOAD feature of the R package in Perl.
# It will call the sum function directly from R::sum().

&R::initR("--silent");
$x = &R::sum(1,2,3);
print "Sum = $x\n";

##</code><code>##

# Calculate HWE goodness-of-fit p-value
# Simply for readability of code passed to R
@x = @{ $alleles1 };
@y = @{ $alleles2 };

@fail = qw( FL PF NTC );

# Create a locus for the data, passing to a string in Perl
$loc = &R::callWithNames(
    "locus",
    {
        'allele1',     \@x,   'allele2',  \@y,
        'locus.alias', $site, 'miss.val', \@fail
    }
);

# Calculate HWE for valid sites, otherwise print error
$testForNA = &R::call( "is.na", $loc );
if ( &R::call( "all", $testForNA ) == 1 ) {
    $hwe = "-";
}
else {
    $hwe = &R::call( "hwe", $loc );
    $hwe = sprintf( "%.4f", $hwe->getEl("gof.pval") );

    #&R::call("print", $hwe);
}
return ( $hwe );

##</code><code>##

sub DESTROY {
     my $obj = $_[0];
     print "Destroying R reference object `", $obj->{name}, "'\n";
     R::deleteRReference($_[0]);
     1;
 }