Bio::Tools::Phylo::PAML
ModelResult
Summary
Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML
Package variables
No package variables defined.
Inherit
Synopsis
# get a ModelResult from a PAML::Result object
use Bio::Tools::Phylo::PAML;
my $paml = new Bio::Tools::Phylo::PAML(-file => 'mlc');
my $result = $paml->next_result;
foreach my $model ( $result->get_model_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
Methods
Methods description
Title : new
Usage : my $obj = new Bio::Tools::Phylo::PAML::ModelResult();
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 |
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) |
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) |
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) |
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) |
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) |
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) |
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 |
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 '**' |
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 |
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 |
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 |
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 |
Title : next_tree
Usage : my $tree = $factory->next_tree;
Function: Get the next tree from the factory
Returns : Bio::Tree::TreeI
Args : none |
Title : get_trees
Usage : my @trees = $result->get_trees;
Function: Get all the parsed trees as an array
Returns : Array of trees
Args : none |
Title : add_tree
Usage : $result->add_tree($tree);
Function: Adds a tree
Returns : integer which is the number of trees stored
Args : Bio::Tree::TreeI |
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) |
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) |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($modelnum,$modeldesc,$kappa,
$timeused,$trees,
$pos_sites,$neb_sites,$beb_sites,
$num_site_classes, $shape_params,
$dnds_classes,
$likelihood) = $self->_rearrange([qw(MODEL_NUM
MODEL_DESCRIPTION
KAPPA
TIME_USED
TREES
POS_SITES
NEB_SITES BEB_SITES
NUM_SITE_CLASSES
SHAPE_PARAMS
DNDS_SITE_CLASSES
LIKELIHOOD)],
@args);
if( $trees ) {
if(ref($trees) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize trees");
} else {
foreach my $t ( @$trees ) {
$self->add_tree($t);
}
}
}
$self->{'_treeiterator'} = 0;
if( $pos_sites ) {
if(ref($pos_sites) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize pos_sites");
} else {
foreach my $s ( @$pos_sites ) {
if( ref($s) !~ /ARRAY/i ) {
$self->warn("need an array ref for each entry in the pos_sites object");
next;
}
$self->add_pos_selected_site(@$s);
}
}
}
if( $beb_sites ) {
if(ref($beb_sites) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize beb_sites");
} else {
foreach my $s ( @$beb_sites ) {
if( ref($s) !~ /ARRAY/i ) {
$self->warn("need an array ref for each entry in the beb_sites object");
next;
}
$self->add_BEB_pos_selected_site(@$s);
}
}
}
if( $neb_sites ) {
if(ref($neb_sites) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize neb_sites");
} else {
foreach my $s ( @$neb_sites ) {
if( ref($s) !~ /ARRAY/i ) {
$self->warn("need an array ref for each entry in the neb_sites object");
next;
}
$self->add_NEB_pos_selected_site(@$s);
}
}
}
defined $modelnum && $self->model_num($modelnum);
defined $modeldesc && $self->model_description($modeldesc);
defined $kappa && $self->kappa($kappa);
defined $timeused && $self->time_used($timeused);
defined $likelihood && $self->likelihood($likelihood);
$self->num_site_classes($num_site_classes || 0);
if( defined $dnds_classes ) {
if( ref($dnds_classes) !~ /HASH/i ||
! defined $dnds_classes->{'p'} ||
! defined $dnds_classes->{'w'} ) {
$self->warn("-dnds_site_classes expects a hashref with keys p and w");
} else {
$self->dnds_site_classes($dnds_classes);
}
}
if( defined $shape_params ) {
if( ref($shape_params) !~ /HASH/i ) {
$self->warn("-shape_params expects a hashref not $shape_params\n");
} else {
$self->shape_params($shape_params);
}
}
return $self;} | sub model_num
{ my $self = shift;
return $self->{'_num'} = shift if @_;
return $self->{'_num'};} | sub model_description
{ my $self = shift;
return $self->{'_model_description'} = shift if @_;
return $self->{'_model_description'};} | sub time_used
{ my $self = shift;
return $self->{'_time_used'} = shift if @_;
return $self->{'_time_used'};} | sub kappa
{ my $self = shift;
return $self->{'_kappa'} = shift if @_;
return $self->{'_kappa'};} | sub num_site_classes
{ my $self = shift;
return $self->{'_num_site_classes'} = shift if @_;
return $self->{'_num_site_classes'};} | sub dnds_site_classes
{ my $self = shift;
return $self->{'_dnds_site_classes'} = shift if @_;
return $self->{'_dnds_site_classes'};} | sub get_pos_selected_sites
{ return @{$_[0]->{'_posselsites'} || []};} | sub add_pos_selected_site
{ my ($self,$site,$aa,$pvalue,$signif) = @_;
push @{$self->{'_posselsites'}}, [ $site,$aa,$pvalue,$signif ];
return scalar @{$self->{'_posselsites'}};} | sub get_NEB_pos_selected_sites
{ return @{$_[0]->{'_NEBposselsites'} || []};} | sub add_NEB_pos_selected_site
{ my ($self,@args) = @_;
push @{$self->{'_NEBposselsites'}}, [ @args ];
return scalar @{$self->{'_NEBposselsites'}};} | sub get_BEB_pos_selected_sites
{ return @{$_[0]->{'_BEBposselsites'} || []};} | sub add_BEB_pos_selected_site
{ my ($self,@args) = @_;
push @{$self->{'_BEBposselsites'}}, [ @args ];
return scalar @{$self->{'_BEBposselsites'}};} | sub next_tree
{ my ($self,@args) = @_;
return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;} | sub get_trees
{ my ($self) = @_;
return @{$self->{'_trees'} || []};} | sub rewind_tree_iterator
{ shift->{'_treeiterator'} = 0;} | sub add_tree
{ my ($self,$tree) = @_;
if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
push @{$self->{'_trees'}},$tree;
}
return scalar @{$self->{'_trees'}};} | sub shape_params
{ my $self = shift;
return $self->{'_shape_params'} = shift if @_;
return $self->{'_shape_params'};} | sub likelihood
{ my $self = shift;
return $self->{'likelihood'} = shift if @_;
return $self->{'likelihood'};} | General documentation
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
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 | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : rewind_tree_iterator
Usage : $result->rewind_tree()
Function: Rewinds the tree iterator so that next_tree can be
called again from the beginning
Returns : none
Args : none