Provided by: libbio-perl-perl_1.6.901-2_all bug

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, "\n";
           print $model->kappa, "\n";
           print $model->run_time, "\n";
       # if you are using PAML < 3.15 then only one place for POS sites
          for my $sites ( $model->get_pos_selected_sites ) {
           print join("\t",@$sites),"\n";
          }
       # otherwise query NEB and BEB slots
          for my $sites ( $model->get_NEB_pos_selected_sites ) {
            print join("\t",@$sites),"\n";
          }

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

         }

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)