Bio::Tools::Phylo::PAML::ModelResult(3pm)

NAME

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

VERSION

version 1.7.3

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";
   }
  }

METHODS

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)

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.

  [email protected]              - General discussion
  http://bioperl.org/Support.html    - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected]

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 the web:

  https://github.com/bioperl/bio-tools-phylo-paml/issues

AUTHOR

Jason Stajich <[email protected]>

COPYRIGHT

This software is copyright (c) by Jason Stajich <[email protected]>.

This software is available under the same terms as the perl 5 programming language system itself.