Bio::Tools::Phylo::PAML::ModelResult(3pm)		User Contributed Perl Documentation		 Bio::Tools::Phylo::PAML::ModelResult(3pm)

NAME

       Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML

SYNOPSIS

	 # get a ModelResult from a PAML::Result object
	 use Bio::Tools::Phylo::PAML;
	 my $paml = Bio::Tools::Phylo::PAML->new(-file => 'mlc');
	 my $result = $paml->next_result;
	 foreach my $model ( $result->get_NSSite_results ) {
	   print $model->model_num, " ", $model->model_description, "
";
	   print $model->kappa, "
";
	   print $model->run_time, "
";
       # if you are using PAML < 3.15 then only one place for POS sites
	  for my $sites ( $model->get_pos_selected_sites ) {
	   print join("	",@$sites),"
";
	  }
       # otherwise query NEB and BEB slots
	  for my $sites ( $model->get_NEB_pos_selected_sites ) {
	    print join("	",@$sites),"
";
	  }

	  for my $sites ( $model->get_BEB_pos_selected_sites ) {
	   print join("	",@$sites),"
";
	  }

	 }

DESCRIPTION

       Describe the object here

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       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 Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via
       email or the web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@open-bio.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::Phylo::PAML::ModelResult->new();
	Function: Builds  a new Bio::Tools::Phylo::PAML::ModelResult object
	Returns : an instance of Bio::Tools::Phylo::PAML::ModelResult
	Args	: -model_num	       => model number
		  -model_description   => model description
		  -kappa	       => value of kappa
		  -time_used	       => amount of time
		  -pos_sites	       => arrayref of sites under positive selection
		  -neb_sites	       => arrayref of sites under positive selection (by NEB analysis)
		  -beb_sites	       => arrayref of sites under positive selection (by BEB analysis)
		  -trees	       => arrayref of tree(s) data for this model
		  -shape_params        => hashref of parameters
					  ('shape' => 'alpha',
					   'gamma' => $g,
					   'r' => $r,
					   'f' => $f
					   )
					   OR
					   ( 'shape' => 'beta',
					     'p' => $p,
					     'q' => $q
					    )
		  -likelihood	       => likelihood
		  -num_site_classes    => number of site classes
		  -dnds_site_classes   => hashref with two keys, 'p' and 'w'
					  which each point to an array, each
					  slot is for a different site class.
					  'w' is for dN/dS and 'p' is probability

   model_num
	Title	: model_num
	Usage	: $obj->model_num($newval)
	Function: Get/Set the Model number (0,1,2,3...)
	Returns : value of model_num (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   model_description
	Title	: model_description
	Usage	: $obj->model_description($newval)
	Function: Get/Set the model description
		  This is something like 'one-ratio', 'neutral', 'selection'
	Returns : value of description (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   time_used
	Title	: time_used
	Usage	: $obj->time_used($newval)
	Function: Get/Set the time it took to run this analysis
	Returns : value of time_used (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   kappa
	Title	: kappa
	Usage	: $obj->kappa($newval)
	Function: Get/Set kappa (ts/tv)
	Returns : value of kappa (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   num_site_classes
	Title	: num_site_classes
	Usage	: $obj->num_site_classes($newval)
	Function: Get/Set the number of site classes for this model
	Returns : value of num_site_classes (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   dnds_site_classes
	Title	: dnds_site_classes
	Usage	: $obj->dnds_site_classes($newval)
	Function: Get/Set dN/dS site classes, a hashref
		  with 2 keys, 'p' and 'w' which point to arrays
		  one slot for each site class.
	Returns : value of dnds_site_classes (a hashref)
	Args	: on set, new value (a scalar or undef, optional)

   get_pos_selected_sites
	Title	: get_pos_selected_sites
	Usage	: my @sites = $modelresult->get_pos_selected_sites();
	Function: Get the sites which PAML has identified as under positive
		  selection (w > 1).  This returns an array with each slot
		  being a site, 4 values,
		  site location (in the original alignment)
		  Amino acid	(I *think* in the first sequence)
		  P		(P value)
		  Significance	(** indicated > 99%, * indicates >=95%)
	Returns : Array
	Args	: none

   add_pos_selected_site
	Title	: add_pos_selected_site
	Usage	: $result->add_pos_selected_site($site,$aa,$pvalue,$signif);
	Function: Add a site to the list of positively selected sites
	Returns : count of the number of sites stored
	Args	: $site   - site number (in the alignment)
		  $aa	  - amino acid under selection
		  $pvalue - float from 0->1 represent probability site is under selection according to this model
		  $signif - significance (coded as either empty, '*', or '**'

   get_NEB_pos_selected_sites
	Title	: get_NEB_pos_selected_sites
	Usage	: my @sites = $modelresult->get_NEB_pos_selected_sites();
	Function: Get the sites which PAML has identified as under positive
		  selection (w > 1) using Naive Empirical Bayes.
		  This returns an array with each slot being a site, 4 values,
		  site location (in the original alignment)
		  Amino acid	(I *think* in the first sequence)
		  P		(P value)
		  Significance	(** indicated > 99%, * indicates > 95%)
		  post mean for w
	Returns : Array
	Args	: none

   add_NEB_pos_selected_site
	Title	: add_NEB_pos_selected_site
	Usage	: $result->add_NEB_pos_selected_site($site,$aa,$pvalue,$signif);
	Function: Add a site to the list of positively selected sites
	Returns : count of the number of sites stored
	Args	: $site   - site number (in the alignment)
		  $aa	  - amino acid under selection
		  $pvalue - float from 0->1 represent probability site is under selection according to this model
		  $signif - significance (coded as either empty, '*', or '**'
		  $postmean - post mean for w

   get_BEB_pos_selected_sites
	Title	: get_BEB_pos_selected_sites
	Usage	: my @sites = $modelresult->get_BEB_pos_selected_sites();
	Function: Get the sites which PAML has identified as under positive
		  selection (w > 1) using Bayes Empirical Bayes.
		  This returns an array with each slot being a site, 6 values,
		  site location (in the original alignment)
		  Amino acid	(I *think* in the first sequence)
		  P		(P value)
		  Significance	(** indicated > 99%, * indicates > 95%)
		  post mean for w (mean)
		  Standard Error for w (SE)
	Returns : Array
	Args	: none

   add_BEB_pos_selected_site
	Title	: add_BEB_pos_selected_site
	Usage	: $result->add_BEB_pos_selected_site($site,$aa,$pvalue,$signif);
	Function: Add a site to the list of positively selected sites
	Returns : count of the number of sites stored
	Args	: $site   - site number (in the alignment)
		  $aa	  - amino acid under selection
		  $pvalue - float from 0->1 represent probability site is under selection according to this model
		  $signif - significance (coded as either empty, '*', or '**'
		  $postmean - post mean for w
		  $SE	    - Standard Error for w

   next_tree
	Title	: next_tree
	Usage	: my $tree = $factory->next_tree;
	Function: Get the next tree from the factory
	Returns : L<Bio::Tree::TreeI>
	Args	: none

   get_trees
	Title	: get_trees
	Usage	: my @trees = $result->get_trees;
	Function: Get all the parsed trees as an array
	Returns : Array of trees
	Args	: none

   rewind_tree_iterator
	Title	: rewind_tree_iterator
	Usage	: $result->rewind_tree_iterator()
	Function: Rewinds the tree iterator so that next_tree can be
		  called again from the beginning
	Returns : none
	Args	: none

   add_tree
	Title	: add_tree
	Usage	: $result->add_tree($tree);
	Function: Adds a tree
	Returns : integer which is the number of trees stored
	Args	: L<Bio::Tree::TreeI>

   shape_params
	Title	: shape_params
	Usage	: $obj->shape_params($newval)
	Function: Get/Set shape params for the distribution, 'alpha', 'beta'
		  which is a hashref
		  with 1 keys, 'p' and 'q'
	Returns : value of shape_params (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   likelihood
	Title	: likelihood
	Usage	: $obj->likelihood($newval)
	Function: log likelihood
	Returns : value of likelihood (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

perl v5.14.2							    2012-03-02				 Bio::Tools::Phylo::PAML::ModelResult(3pm)