Raw content of Bio::EnsEMBL::AffyProbe
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::AffyProbe - A module to represent an Affymetrix probe.
=head1 SYNOPSIS
use Bio::EnsEMBL::OligoProbe;
my $probe = Bio::EnsEMBL::OligoProbe->new(
-PROBENAME => 'Probe-1',
-ARRAY => $array,
-PROBESET => 'Probeset-1',
);
=head1 DESCRIPTION
An AffyProbe object represents an Affy probe on a microarray. The
data (currently the name, array, length, probeset and description) are
stored in the oligo_probe table. The complete name of a probe is the
concatenation of the array name, the probeset and the probe name.
For Affy arrays, a probe can be part of more than one array, but
only part of one probeset. 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 oligo_probe_id. Thus the same Affy probe can have a
number of different names and complete names depending on which array
it's on.
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::AffyProbe;
use Bio::EnsEMBL::Utils::Exception qw( warning );
use Bio::EnsEMBL::OligoProbe;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::OligoProbe);
=head2 new
Arg [-PROBENAME] : string - probe name
Used when the probe is on one array. Can also use -NAME.
Arg [-PROBENAMES] : Listref of strings - probe names
Used when the probe is on multiple arrays. Can also use -NAMES.
Arg [-ARRAY] : Bio::EnsEMBL::AffyArray
or [-ARRAYNAME] : string - array name
Used when the probe is on one array. Either -ARRAY or -ARRAYNAME can be
used. The latter is a convenience and -ARRAY must be used if the probe
is to be stored.
Arg [-ARRAYS] : Listref of Bio::EnsEMBL::AffyArray objects
or [-ARRAYNAMES] : Listref of strings - array names
Used when the probe is on multiple arrays. Either -ARRAYS or
-ARRAYNAMES can be used. The latter is a convenience and -ARRAYS must
be used if the probes are to be stored.
Arg [-PROBESET] : string - probeset name
Each probe is part of one (and only one) probeset.
Arg [-PROBELENGTH]: int - probe length
Like probesets, will obviously be the same for all probes if same probe
is on multiple arrays.
Arg [-DESCRIPTION]: string - probe description
Like probesets, will be the same for all probes if same probe is on
multiple arrays.
Example : my $probe = Bio::EnsEMBL::AffyProbe->new(
-PROBENAME => 'Probe-1',
-ARRAY => $array,
-PROBESET => 'Probeset-1',
);
Description: Creates a new Bio::EnsEMBL::AffyProbe object.
Returntype : Bio::EnsEMBL::AffyProbe
Exceptions : Throws if not supplied with probe name(s) and array(s)
Caller : General
Status : Medium Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
# Affy probes are 25mers (unless otherwise specified)
if ( !$self->probelength() ) {
$self->probelength(25);
}
return $self;
}
=head2 get_all_AffyFeatures
Args : None
Example : my $features = $probe->get_all_AffyFeatures();
Description: Get all features produced by this probe. The probe needs to be
database persistent.
Returntype : Listref of Bio::EnsEMBL:AffyFeature objects
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub get_all_AffyFeatures {
my $self = shift;
if ( $self->adaptor() && $self->dbID() ) {
return $self->adaptor()->db()->get_AffyFeatureAdaptor()->fetch_all_by_AffyProbe($self);
} else {
warning('Need database connection to retrieve Features');
return [];
}
}
=head2 get_all_AffyArrays
Args : None
Example : my $arrays = $probe->get_all_AffyArrays();
Description: Returns all arrays that this probe is part of. Only works if the
probe was retrieved from the database or created using
add_Array_probename (rather than add_arrayname_probename).
Returntype : Listref of Bio::EnsEMBL::AffyArray objects
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub get_all_AffyArrays {
my $self = shift;
return $self->get_all_Arrays();
}
1;
]]>