Bio::EnsEMBL::Funcgen
ProbeSet
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Summary
Bio::EnsEMBL::Funcgen::ProbeSet - A module to represent a probeset.
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::EnsEMBL::Funcgen::ProbeSet;
#
my $probe = Bio::EnsEMBL::Funcgen::ProbeSet->new(
-NAME => 'ProbeSet-1',
-SIZE => 1,
-FAMILY => "ENCODE REGIONS",
);
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.
Methods
Methods description
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 |
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 |
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 |
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 |
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 |
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 |
Methods code
| add_Array_probename | description | prev | next | Top |
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;} | sub family
{ my $self = shift;
$self->{'family'} = shift if @_;
return $self->{'family'};} | sub get_all_Arrays
{ my $self = shift;
throw("get_all_Arrays not implemented yet");
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_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 [];
}} | sub name
{ my $self = shift;
$self->{'name'} = shift if @_;
return $self->{'name'};} | sub new
{ my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
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; } | sub size
{ my $self = shift;
$self->{'size'} = shift if @_;
return $self->{'size'};
}
1;} | General documentation
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:
/
| add_Array_probeset_name | Top |
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