Bio SearchDist
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object
Package variables
No package variables defined.
Inherit
Bio::Root::Root
Synopsis
  $dis = Bio::SearchDist->new();
foreach $score ( @scores ) {
$dis->add_score($score);
}
if( $dis->fit_evd() ) { foreach $score ( @scores ) { $evalue = $dis->evalue($score); print "Score $score had an evalue of $evalue\n"; } } else { warn("Could not fit histogram to an EVD!"); }
Description
The Bio::SearchDist object is a wrapper around Sean Eddy's excellent
histogram object. The histogram object can bascially take in a number
of scores which are sensibly distributed somewhere around 0 that come
from a supposed Extreme Value Distribution. Having add all the scores
from a database search via the add_score method you can then fit a
extreme value distribution using fit_evd(). Once fitted you can then
get out the evalue for each score (or a new score) using
evalue($score).
The fitting procedure is better described in Sean Eddy's own code
(available from http://hmmer.janelia.org/, or in the histogram.h header
file in Compile/SW). Bascially it fits a EVD via a maximum likelhood
method with pruning of the top end of the distribution so that real
positives are discarded in the fitting procedure. This comes from
an orginally idea of Richard Mott's and the likelhood fitting
is from a book by Lawless [should ref here].
The object relies on the fact that the scores are sensibly distributed
around about 0 and that integer bins are sensible for the
histogram. Scores based on bits are often ideal for this (bits based
scoring mechanisms is what this histogram object was originally
designed for).
Methods
BEGIN Code
new
No description
Code
add_scoreDescriptionCode
fit_evdDescriptionCode
fit_GaussianDescriptionCode
evalueDescriptionCode
_engineDescriptionCode
Methods description
add_scorecode    nextTop
 Title   : add_score
Usage : $dis->add_score(300);
Function: Adds a single score to the distribution
Returns : nothing
Args :
fit_evdcodeprevnextTop
 Title   : fit_evd
Usage : $dis->fit_evd();
Function: fits an evd to the current distribution
Returns : 1 if it fits successfully, 0 if not
Args :
fit_GaussiancodeprevnextTop
 Title   : fit_Gaussian
Usage :
Function:
Example :
Returns :
Args :
evaluecodeprevnextTop
 Title   : evalue
Usage : $eval = $dis->evalue($score)
Function: Returns the evalue of this score
Returns : float
Args :
_enginecodeprevnextTop
 Title   : _engine
Usage : $obj->_engine($newval)
Function: underlyine bp_sw:: histogram engine
Returns : value of _engine
Args : newvalue (optional)
Methods code
BEGINTop
BEGIN {
    eval {
	require Bio::Ext::Align;
    };
    if ( $@ ) {
print $@;
	print STDERR ("\nThe C-compiled engine for histogram object (Bio::Ext::Align) has not been installed.\n Please install the bioperl-ext package\n\n");
	exit(1);
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  my($min, $max, $lump) =
	$self->_rearrange([qw(MIN MAX LUMP)], @args);

  if( !  $min ) {
    $min = -100;
  }

  if( !  $max ) {
    $max = +100;
  }

  if( ! $lump ) {
    $lump = 50;
  }

  $self->_engine(&Bio::Ext::Align::new_Histogram($min,$max,$lump));

  return $self;
}
add_scoredescriptionprevnextTop
sub add_score {
   my ($self,$score) = @_;
   my ($eng);
   $eng = $self->_engine();
   #$eng->AddToHistogram($score);
$eng->add($score);
}
fit_evddescriptionprevnextTop
sub fit_evd {
   my ($self,@args) = @_;

   return $self->_engine()->fit_EVD(10000,1);
}
fit_GaussiandescriptionprevnextTop
sub fit_Gaussian {
   my ($self,$high) = @_;

   if( ! defined $high ) {
       $high = 10000;
   }

   return $self->_engine()->fit_Gaussian($high);
}
evaluedescriptionprevnextTop
sub evalue {
   my ($self,$score) = @_;

   return $self->_engine()->evalue($score);
}
_enginedescriptionprevnextTop
sub _engine {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'_engine'} = $value;
    }
    return $self->{'_engine'};
}


## End of Package
1; __END__
}
General documentation
CONTACTTop
The original code this was based on comes from the histogram module as
part of the HMMer2 package. Look at http://hmmer.janelia.org/
Its use in Bioperl is via the Compiled XS extension which is cared for
by Ewan Birney (birney@ebi.ac.uk). Please contact Ewan first about
the use of this module
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _