Raw content of Bio::EnsEMBL::Funcgen::ProbeSet
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# Ensembl module for Bio::EnsEMBL::Funcgen::ProbeSet
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::Funcgen::ProbeSet - A module to represent a probeset.
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::ProbeSet;
#
my $probe = Bio::EnsEMBL::Funcgen::ProbeSet->new(
-NAME => 'ProbeSet-1',
-SIZE => 1,
-FAMILY => "ENCODE REGIONS",
);
=head1 DESCRIPTION
A ProbeSet object represents a set of probes on a microarray. The
data (currently the name, size, and family) are stored in the probe_set
table. ProbeSets are only really relevant for Affy probes, or when
avaliable these will be analagous to Nimblegen feature sets.
For Affy arrays, a probeset can be part of more than one array, containing unique
probes.
#Need to rewrite this bit
#Something about array_chip_id i.e. experimental validation etc
On each Affy array the probe has a slightly different name. For
example, two different complete names for the same probe might be
DrosGenome1:AFFX-LysX-5_at:535:35; and Drosophila_2:AFFX-LysX-5_at:460:51;. In
the database, these two probes will have the same probe_id. Thus the same
Affy probe can have a number of different names and complete names depending on
which array it is on.
=head1 AUTHOR
This module was created by Nathan Johnson, but is almost entirely based on the
AffyProbe module written by Ian Sealy and Arne Stabenau.
This module is part of the Ensembl project: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::ProbeSet;
use Bio::EnsEMBL::Utils::Argument qw( rearrange ) ;
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Storable;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [-NAME] : string - probeset name
Arg [-SIZE] : int - probe set size
Will be the same for all probes sets if same probe set
is on multiple arrays.
Arg [-FAMILY] : string - probe set family, generic descriptor for probe set e.g. ENCODE REGIONS, RANDOM
Will be the same for all probes sets if same probe set is on multiple arrays.
Example : my $probeset = Bio::EnsEMBL::Funcgen::ProbeSet->new(
-NAME => 'ProbeSet-1',
-SIZE => 1,
-FAMILY => "ENCODE_REGIONS",
);
Description: Creates a new Bio::EnsEMBL::Funcgen::ProbeSet object.
Returntype : Bio::EnsEMBL::Funcgen::ProbeSet
Exceptions : Throws if not supplied with probeset name and array chip id(s)
Caller : General
Status : Medium Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
#warn("The only way to get array names/ids, is to retrieve all the probes!!!");
my (
$name, $size,
$family
) = rearrange([
'NAME', 'SIZE',
'FAMILY',
], @_);
$self->name($name) if defined $name;
$self->family($family) if defined $family;
$self->size($size) if defined $size;
return $self;
}
=head2 add_Array_probeset_name
Arg [1] : Bio::EnsEMBL::Array - array
Arg [2] : string - probeset name
Example : $probe->add_Array_probeset_name($array, $probename);
Description: Adds a probeset name / array pair to a probeset, allowing incremental
generation of a probeset.
Returntype : None
Exceptions : None
Caller : General,
ProbeSet->new(),
ProbeSetAdaptor->_obj_from_sth(),
Status : Medium Risk
=cut
sub add_Array_probename {
my $self = shift;
throw("Not implemented");
my ($array, $probeset_name) = @_;
$self->{ 'arrays' } ||= {};
$self->{ 'arrays' }->{$array->name()} = $array;
$self->{ 'probesetnames' }->{$array->name()} = $probeset_name;
}
=head2 get_all_ProbeFeatures
Args : None
Example : my $features = $probeset->get_all_ProbeFeatures();
Description: Get all features produced by this probeset. The probeset needs to be
database persistent.
Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeFeature objects
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub get_all_ProbeFeatures {
my $self = shift;
throw("Not implemented yet, do we want to do this for ProbeSet or just probe?");
if ( $self->adaptor() && $self->dbID() ) {
return $self->adaptor()->db()->get_ProbeFeatureAdaptor()->fetch_all_by_ProbeSet($self);
} else {
warning('Need database connection to retrieve Features');
return [];
}
}
=head2 get_all_Arrays
Args : None
Example : my $arrays = $probeset->get_all_Arrays();
Description: Returns all arrays that this probeset is part of. Only works if the
probedet was retrieved from the database or created using
add_Array_probename.
Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub get_all_Arrays {
my $self = shift;
throw("get_all_Arrays not implemented yet");
# Do we have Array objects for this probe?
if (defined $self->{'arrays'}) {
return [ values %{$self->{'arrays'}} ];
} elsif ( $self->adaptor() && $self->dbID() ) {
warning('Not yet implemented, need to get Arrays from array_chip_ids');
return [];
} else {
warning('Need database connection to get Arrays by name');
return [];
}
}
#sub get_all_array_chips_ids?
#sub get_all_Results? from_Experiment?
=head2 name
Arg [1] : string - aprobeset name
Example : my $probesetname = $probeset->name('probeset-1');
Description: Getter/Setter for the name attribute of ProbeSet objects.
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub name {
my $self = shift;
$self->{'name'} = shift if @_;
return $self->{'name'};
}
=head2 family
Arg [1] : (optional) string - family
Example : my $family = $probe->family();
Description: Getter and setter of family attribute for ProbeSet
objects. e.g. EXPERIMENTAL or CONTROL
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub family {
my $self = shift;
$self->{'family'} = shift if @_;
return $self->{'family'};
}
=head2 size
Arg [1] : (optional) int - probeset size
Example : my $probeset_size = $probeset->size();
Description: Getter and setter of probeset size attribute for ProbeSet
objects.
Returntype : int
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub size {
my $self = shift;
$self->{'size'} = shift if @_;
return $self->{'size'};
}
1;
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