Provided by: libbio-perl-perl_1.6.923-1_all 
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)