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  $obj->pathways[($order)];
  $obj->pathway_result($pathway, $data_name[, $all_flag]);
  $obj->pathway_desc($pathway);
  $obj->pathway_genes($pathway);
  $obj->fdr_position($fdr);

=head3 Other Methods

  $obj->gene_count[($fet_gene_count)];
  $obj->calculate;

=head1 DESCRIPTION

Bio::FdrFet implements the False Discovery Rate Fisher Exact Test of gene
expression analysis applied to pathways described in the paper by
Ruiru Ji, Karl-Heinz Ott, Roumyana Yordanova, and Robert E
Bruccoleri.  A copy of the paper is included with the distribution in
the file, Fdr-Fet-Manuscript.pdf.

The module is implemented using a simple object oriented paradigm
where the object stores all the information needed for a calculation
along with a state variable, C<STATE>. The state variable has two
possible values, C<'setup'> and C<'calculated'>. The value of
C<'setup'> indicates that the object is being setup with data, and any
results in the object are inconsistent with the data. The value of
C<'calculated'> indicates that the object's computational results are
consistent with the data, and may be returned to a calling program.

The C<'calculate'> method is used to update all the calculated values
from the input data. It checks the state variable first, and only does
the calculation if the state is C<'setup'>. Once the calculations are
complete, then the state variable is set to C<'calculated'>. Thus, the C<calculate> method
can be called whenever a calculated value is needed, and there is no
performance penalty.

The module initializes the C<Bio::FdrFet> object with a state of
C<'setup'>. Any data input sets the state to C<'setup'>. Any requests
for calculated data, calls C<'calculate'>, which updates the state
variable so futures requests for calculated data return quickly.

=head1 METHODS

The following methods are provided:

=over 4

=cut


=item C<new([$fdrcutoff])>

Creates a new Bio::FdrFet object. The optional parameter is the False
Discovery Rate cutoff in units of percent. See the C<fdr_cutoff>
method below for more details.

=cut

sub new {
    my $pkg;
    my $class = shift;
    eval {($pkg) = caller(0);};
    if ($class ne $pkg) {
	unshift @_, $class;
    }
    my $self = {};
    bless $self;
    my $cutoff = shift;
    $cutoff = 35 if not defined $cutoff;
    $self->{STATE} = "setup";
    $self->{FDR_CUTOFF} = _check_fdr_cutoff($cutoff);
    $self->{PATHWAYS} = {};
    $self->{GENES} = {};
    $self->{INPUT_GENE_COUNT} = 0;
    $self->{GENE_COUNT} = undef;
    $self->{VERBOSE} = 1;
    $self->{UNIVERSE} = "genes";
    return $self;
}

=item C<fdr_cutoff([$fdrcutoff])>

Retrieves the current setting for the False Discovery Rate threshold,
and optionally sets it. This threshold must be an integer greater than
0 and less than or equal to 100, and is divided by 100 for the value
used by the computation.

=cut

sub fdr_cutoff {

    my $self = shift;
    my $new_cutoff = shift;
    if (defined($new_cutoff)) {
	$self->{FDR_CUTOFF} = _check_fdr_cutoff($new_cutoff);
        $self->{STATE} = 'setup';
    }
    return $self->{FDR_CUTOFF};
}

=item C<verbose([$verbose_mode])>

Retrieves the current setting for the verbose parameter
and optionally sets it. It can be either 0, no verbosity, or 1, lots
of messages sent to STDERR.

=cut

sub verbose {

    my $self = shift;
    my $new_verbose = shift;
    if (defined($new_verbose)) {
	$self->{VERBOSE} = $new_verbose;
    }
    return $self->{VERBOSE};
}

=item C<universe([$universe_option])>

Retrieves the current setting for the B<universe> option
and optionally sets it. The B<universe> option specifies how the number of