UniqueFeature

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Data Stream Processing > Processing Modules > Clustering and collation Modules

Description

The UniqueFeature processing module is clustering style module which combines Features which match a unique or identical criteria.
The basic criteria for Features being unique is that they share the same genomic location (chrom/start/end) including the same strand.

Parameters

  • <ignore_strand> : if true then features can be on different strands, but still be consider identical as long as they have the same start/end/chrom location.
  • <match_category> : if true then features must also have same FeatureSource category to be classified as identical, but do not need to be from exact same FeatureSource.
  • <match_source> : if true then features must also have same FeatureSource to be classified as identical.
  • <expression_mode> : defines how expression within matching Experiments between unique features are collated together. Possible values are:
    • sum : sum the expression between multiple primary stream features for each matching experiment into the unique feature
    • min : calculate the minimum expression value between multiple primary stream features for each matching experiment
    • max : calculate the minimum expression value between multiple primary stream features for each matching experiment
    • count : count the number of primary stream features for each matching experiment overlapping the unique feature.
    • mean : calculate the average expression value among primary stream features for each matching experiment overlapping the unique feature

Example

This is a script which incorporates a CalcInterSubfeatures, StreamSubfeatures, UniqueFeature followed by CutoffFilter to generate a set of unique introns which can be displayed with score coloring.

<zenbu_script>
	<stream_processing>
		<spstream module="CalcInterSubfeatures"/>
		<spstream module="StreamSubfeatures">
			<category_filter>intron</category_filter>
		</spstream>
		<spstream module="UniqueFeature">
			<ignore_strand>true</ignore_strand>
		</spstream>
		<spstream module="CutoffFilter">
			<min_cutoff>2</min_cutoff>
		</spstream>
	</stream_processing>
</zenbu_script>

second variation on this script using the internal unique-feature controls of the StreamSubfeatures rather than an external UniqueFeature module

<zenbu_script>
	<stream_processing>
		<spstream module="CalcInterSubfeatures"/>
		<spstream module="StreamSubfeatures">
			<category_filter>intron</category_filter>
			<unique>
				<ignore_strand>true</ignore_strand>
			</unique>
		</spstream>
		<spstream module="CutoffFilter">
			<min_cutoff>2</min_cutoff>
		</spstream>
	</stream_processing>
</zenbu_script>

Example ZENBU view showing this script in use
http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=X_wwpjePN9Qi8bqoMur8TB;loc=hg19::chr8:128746973..128755020