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 hereFEEDBACK
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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:
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AUTHOR - Jason Stajich
Email [email protected]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)