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Bio::Map::Prediction.3pm
Langue: en
Version: 2009-02-27 (fedora - 06/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Map::Prediction - An object representing the predictions of something that can have multiple locations in several maps.SYNOPSIS
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;
DESCRIPTION
For example, used to model transcription factor binding site predictions, which can have multiple locations in several maps.FEEDBACK
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AUTHOR - Sendu Bala
Email bix@sendu.me.ukAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
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
source
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
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