Summary

TFBS::PatternGen::Gibbs::Motif - class for unprocessed motifs and associated
numerical scores created by the Gibbs program

Package variables

Included modules

Inherit

TFBS::PatternGen::Motif::Matrix

Synopsis

Description

TFBS::PatternGen::Gibbs::Motif is used to store and manipulate unprocessed
motifs and associated numerical scores created by the Gibbs program. You do not
normally want to create a TFBS::PatternGen::Gibbs::Motif yourself. They are created
by running TFBS::PatternGen::Gibbs

Methods

Methods description

 Title   : MAP
 Usage   : my $map_score = $motif->MAP;
 Function: returns MAP score for the detected motif
	   (This is a backward compatibility method. For consistency,
	    you should use $motif->tag('MAP_score') instead
 Returns : float (a scalar)
 Args    : none

Methods code

sub MAP {

    my ($self) = @_;
    return $self->tag("MAP_score");

}

sub _calculate_PFM {

    my $self = shift;
    unless ($self->{'nr_hits'}) {
	$self->throw(ref($self).
		     " objects must be created with a (nonzero)".
		     " -nr_hits parameter in constructor"
		     );
    }
    my @PFM;
    foreach my $rowref ( @{$self->{'matrix'}} )  {
	my @PFMrow;
	foreach my $element (@$rowref) {
	    push @PFMrow, int($self->{'nr_hits'}*$element/100 + 0.5);
	}
	push @PFM, [@PFMrow];
    }
    return\@ PFM;

}

General documentation

Please send bug reports and other comments to the author.

Boris Lenhard <Boris.Lenhard@cgb.ki.se>
Wynand Alkema <Wynand.Alkema@cgb.ki.se>

The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.

TFBS::PatterGen::Motif::Gibbs inherits from TFBS::PatternGen::Motif,
which inherits from TFBS::Matrix. Please consult the documentation of those modules
for additional available methods.