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.\" ========================================================================
.\"
.IX Title "Bio::SearchDist 3pm"
.TH Bio::SearchDist 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::SearchDist \- A perl wrapper around Sean Eddy's histogram object
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 4
\&  $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 $evalue\en";
\&    }
\&  } else {
\&    warn("Could not fit histogram to an EVD!");
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
The Bio::SearchDist object is a wrapper around Sean Eddy's excellent
histogram object. The histogram object can bascially take in a number
of scores which are sensibly distributed somewhere around 0 that come
from a supposed Extreme Value Distribution. Having add all the scores
from a database search via the add_score method you can then fit a
extreme value distribution using \fIfit_evd()\fR. Once fitted you can then
get out the evalue for each score (or a new score) using
evalue($score).
.PP
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 \s-1EVD\s0 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 originally idea of Richard Mott's and the likelhood fitting
is from a book by Lawless [should ref here].
.PP
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).
.SH "CONTACT"
.IX Header "CONTACT"
The original code this was based on comes from the histogram module as
part of the HMMer2 package. Look at http://hmmer.janelia.org/
.PP
Its use in Bioperl is via the Compiled \s-1XS\s0 extension which is cared for
by Ewan Birney (birney@ebi.ac.uk). Please contact Ewan first about
the use of this module
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "add_score"
.IX Subsection "add_score"
.Vb 5
\& Title   : add_score
\& Usage   : $dis\->add_score(300);
\& Function: Adds a single score to the distribution
\& Returns : nothing
\& Args    :
.Ve
.SS "fit_evd"
.IX Subsection "fit_evd"
.Vb 5
\& 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    :
.Ve
.SS "fit_Gaussian"
.IX Subsection "fit_Gaussian"
.Vb 6
\& Title   : fit_Gaussian
\& Usage   :
\& Function:
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "evalue"
.IX Subsection "evalue"
.Vb 5
\& Title   : evalue
\& Usage   : $eval = $dis\->evalue($score)
\& Function: Returns the evalue of this score
\& Returns : float
\& Args    :
.Ve
.SS "_engine"
.IX Subsection "_engine"
.Vb 5
\& Title   : _engine
\& Usage   : $obj\->_engine($newval)
\& Function: underlyine bp_sw:: histogram engine
\& Returns : value of _engine
\& Args    : newvalue (optional)
.Ve