TFBS::PatternGen::Gibbs
Motif
Summary
TFBS::PatternGen::Gibbs::Motif - class for unprocessed motifs and associated
numerical scores created by the Gibbs program
Package variables
No package variables defined.
Included modules
Inherit
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"); } |
_calculate_PFM | description | prev | next | Top |
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.
AUTHOR - Boris Lenhard and Wynand Alkema | Top |
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.