++ed by:
DEMIAN ILUX PINGAN GENEHACK YUSRIDEB

11 PAUSE users
14 non-PAUSE users.

Christopher Fields
and 1 contributors

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

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHOR - Sendu Bala

Email bix@sendu.me.uk

APPENDIX

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