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NAME - EEDB::Expression

SYNOPSIS

DESCRIPTION

CONTACT

Jessica Severin <severin@gsc.riken.jp>

LICENSE

 * Software License Agreement (BSD License)
 * EdgeExpressDB [eeDB] system
 * copyright (c) 2007-2009 Jessica Severin RIKEN OSC
 * All rights reserved.
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *     * Redistributions of source code must retain the above copyright
 *       notice, this list of conditions and the following disclaimer.
 *     * Redistributions in binary form must reproduce the above copyright
 *       notice, this list of conditions and the following disclaimer in the
 *       documentation and/or other materials provided with the distribution.
 *     * Neither the name of Jessica Severin RIKEN OSC nor the
 *       names of its contributors may be used to endorse or promote products
 *       derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ''AS IS'' AND ANY
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL COPYRIGHT HOLDERS BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

stream_all

  Description: stream all expression (with feature) out of database 
               with a given set of source, experiment and datatype filters
  Arg (1)    : $database (MQdb::Database)
  Arg (2...) : hash named filter parameters. 
                 datatypes=>["tpm","raw"], 
                 sources=>[$fsrc1, $fsrc2,$fsrc3],  instances of EEDB::FeatureSource
                 experiments=>[$exp1, $exp2]  instances of EEDB::Experiment
  Returntype : a DBStream instance
  Exceptions : none 

stream_by_chrom

  Description: stream all expression (with feature) on a specific EEDB::Chrom
               with a given set of source, experiment and datatype filters
  Arg (1)    : $chrom (EEDB::Chrom object with database)
  Arg (2...) : hash named filter parameters. 
                 datatypes=>["tpm","raw"], 
                 sources=>[$fsrc1, $fsrc2,$fsrc3],  instances of EEDB::FeatureSource
                 experiments=>[$exp1, $exp2]  instances of EEDB::Experiment
  Returntype : a DBStream instance
  Exceptions : none 

stream_by_named_region

  Description: stream all expression (with feature) from a specific region on a genome
               with a given set of source, experiment and datatype filters
  Arg (1)    : $database (MQdb::Database)
  Arg (2)    : $assembly_name (string)
  Arg (3)    : $chrom_name (string)
  Arg (4)    : $chrom_start (integer)
  Arg (5)    : $chrom_end (integer)
  Arg (6...) : hash named filter parameters. 
                 datatypes=>["tpm","raw"], 
                 sources=>[$fsrc1, $fsrc2,$fsrc3],  instances of EEDB::FeatureSource
                 experiments=>[$exp1, $exp2]  instances of EEDB::Experiment
  Returntype : a DBStream instance
  Exceptions : none