| Bio::Map::Prediction(3pm) | User Contributed Perl Documentation | Bio::Map::Prediction(3pm) |
Bio::Map::Prediction - An object representing the predictions of something that can have multiple locations in several maps.
use Bio::Map::Prediction;
use Bio::Map::Position;
# normally you would get predictions from a run wrapper like
# Bio::Tools::Run::Meme, but here we create some manually:
my $pred1 = Bio::Map::Prediction->new(-source => 'meme');
Bio::Map::Position->new(-element => $prediction1,
-map => Bio::Map::GeneMap->get(-gene => 'gene1',
-species => 'species1'),
-start => 950,
-end => 960);
Bio::Map::Position->new(-element => $prediction1,
-map => Bio::Map::GeneMap->get(-gene => 'gene1',
-species => 'species2'),
-start => 1950,
-end => 1960);
Bio::Map::Position->new(-element => $prediction1,
-map => Bio::Map::GeneMap->get(-gene => 'gene2',
-species => 'species1'),
-start => 955,
-end => 965);
Bio::Map::Position->new(-element => $prediction1,
-map => Bio::Map::GeneMap->get(-gene => 'gene2',
-species => 'species2'),
-start => 1955,
-end => 1965);
my $pred2 = Bio::Map::Prediction->new(-source => 'gerp');
Bio::Map::Position->new(-element => $prediction2,
-map => Bio::Map::GeneMap->get(-gene => 'gene1',
-species => 'species1'),
-start => 950,
-end => 960);
# etc.
# find the places where predictions agree
use Bio::Map::GeneRelative;
my $rel = Bio::Map::GeneRelative->new(-gene => 0);
my $di = Bio::Map::Mappable->disconnected_intersections([$pred1, $pred2],
-min_mappables_percent => 100,
-min_map_percent => 100,
-relative => $rel);
my @positions = $di->get_positions;
For example, used to model transcription factor binding site predictions, which can have multiple locations in several maps.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $prediction = Bio::Map::Prediction->new();
Function: Builds a new Bio::Map::Prediction object
Returns : Bio::Map::Prediction
Args : -name => string : name of the mappable element
-id => string : id of the mappable element
-source => string : name of the prediction program
Title : name
Usage : $mappable->name($new_name);
my $name = $mappable->name();
Function: Get/Set the name for this Mappable
Returns : A scalar representing the current name of this Mappable
Args : none to get
string to set
| 2018-10-27 | perl v5.26.2 |