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convert(Model) - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

Creates GSEA entries from the pathways contained in the model.

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getAllowedOrganisms() - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

getMinNumOfGenesPerEntry() - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

If this value is greater than 0, and the number of proteins/genes in a gene set is less than that value, then this gene set is to skip (no GSEA entry is written).

GSEAConverter - Class in org.biopax.paxtools.io.gsea

Converts a BioPAX model to the GMT format (used by GSEA software).

GSEAConverter() - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter

Constructor.

GSEAConverter(String, boolean) - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter

Constructor.

GSEAConverter(String, boolean, boolean) - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter

Constructor.

GSEAConverter(String, boolean, Set<Provenance>) - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter

Constructor.

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isSkipOutsidePathways() - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

If true, then only GSEA entries that (genes) correspond to a Pathway are printed to the output.

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org.biopax.paxtools.io.gsea - package org.biopax.paxtools.io.gsea

This package is a tool to convert a BioPAX model to the GMT format, which can be then analysed with the standard GSEA software and other tools (because the result is a simple TSV text).

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setAllowedOrganisms(Set<String>) - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

setMinNumOfGenesPerEntry(int) - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

setSkipOutsidePathways(boolean) - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

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writeToGSEA(Model, OutputStream) - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

Converts model to GSEA (GMT) and writes to out.

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