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Summary

Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME

Package variables

Included modules

Inherit

Bio::EnsEMBL::Analysis::RunnableDB::Funcgen

Synopsis

  my $runnable = Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME->new
     (
         -db       => $db,
         -input_id => 'chromosome::20:1:100000:1',
         -analysis => $analysis,
     );
  $runnable->fetch_input;
  $runnable->run;
  $runnable->write_output;

Description

This module provides an interface between the ensembl functional genomics
database and the Runnable ACME which wraps the R package ACME (for Algorithm
for Capturing Microarray Enrichment).

Methods

Methods description

  Arg [1]     : 
  Arg [2]     : 
  Description : Instantiates new ACME runnabledb
  Returntype  : Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME object
  Exceptions  : 
  Example     :

Methods code

sub new {

    print "Analysis::RunnableDB::Funcgen::ACME::new\n";
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    $self->read_and_check_config($CONFIG);

    # make sure we have the correct analysis object
    $self->check_Analysis();

    # make sure we can store the correct feature_set, data_sets, and result_sets
    $self->check_Sets();

    return $self;
	
}

1;

}

General documentation

Stefan Graf, Ensembl Functional Genomics - /

Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk