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lib/Bio/FdrFet.pm  view on Meta::CPAN

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;

lib/Bio/FdrFet.pm  view on Meta::CPAN

Returns a calculated result for a pathway. The following values may be
used for C<$data_name>. Case of C<$data_name> does not matter.

 LOGPVAL   -log10(probability value for pathway).
 PVAL      probability value for pathway
 ODDS      Odds ratio. 
 Q         Number of genes in the pathway passing the FDR cutoff
 M         Number of genes overall passing the FDR cutoff
 N         Number of genes in the system minus C<M> above.
 K         Number of genes in the pathway.
 FDR       FDR cutoff in percent giving the best pvalue.
 LOCI      Reference to an array of gene names in the pathway
           that satisfy FDR cutoff.

If C<$all_flag> is specified and has the value, "all", then this
returns an array of values for all the attempted FDR cutoffs, except
for the c<FDR> cutoff.

=cut

sub pathway_result {