Proxy

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Revision as of 19:37, 15 May 2012 by Jessica Severin (talk | contribs) (Example)
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Description

The FilterSubfeatures processing module is designed to work on Features with subfeatures to remove subfeatures not specified in the category filtering and then rebuild the outer feature boundaries based on the remaining subfeatures. The module will resort features on the data stream as needed to preserve the stream integrity.

Atributes

Proxy is a special module in the system and does not have parameters. Instead it has a single attribute

  • name : name of the <datastream> which will be injected in place of this proxy at query time.

Example

This is a script which incorporates a Proxy / TemplateCluster to collate expression into Gencode V10 gene models. The expression is then normalized via theNormalizeRPKM module. The script finishes with CalcFeatureSignificance so that the Features can be displayed via score-coloring.

<zenbu_script>
	<datastream name="gencode">
		<source id="D71B7748-1450-4C62-92CB-7E913AB12899::19:::FeatureSource"/>
	</datastream>
	<stream_queue>
		<spstream module="TemplateCluster">
			<overlap_mode>height</overlap_mode>
			<skip_empty_templates>false</skip_empty_templates>
			<expression_mode>sum</expression_mode>
			<overlap_subfeatures>true</overlap_subfeatures>
			<ignore_strand>true</ignore_strand>
			<side_stream>
				<spstream module="EEDB::SPStream::Proxy" name="gencode"/>
			</side_stream>
		</spstream>

		<spstream module="NormalizeRPKM"/>

		<spstream module="CalcFeatureSignificance"/>
	</stream_queue>
</zenbu_script>

Here is a ZENBU view showing this script in use
http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=vtPXLwwqO9KjD1YYWqCMGD;loc=hg19::chr8:128746973..128755020