Rechercher une page de manuel
Bio::Tools::Phylo::PAML::ModelResult.3pm
Langue: en
Version: 2010-05-19 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAMLSYNOPSIS
# 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
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:http://bugzilla.open-bio.org/
AUTHOR - Jason Stajich
Email jason@open-bio.orgAPPENDIX
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)
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre