Export

This program exports sub-networks with GraphML file format. All sub-networks in the input GMT file will collapsed into a GraphML structure. Each gene count is included in the node attribute, 'Count'. You can add genes of your interest in the node attribute, 'Special'. Any numeric properties can be added.

Usage : export [OPTION]
Options:
    -n           name
    -i           gmt file
    -o           output graphml file
    -p           property name = property file pairs (delimited by ':')
    -m           important gene (delimited by ':')
Example: export -n my_network -i input.gmt -o output.graphml -p T-Statistics=GSE8671_samt.csv:FoldChange=GSE8671_foldchange.csv -m 324:3845:7157:5290:55294:114788:63923

Input

Gene Matrix Transposed (GMT) file format

Subnet236	17.9005898844578	87	1030	4128	8850	53405
Subnet2075	17.6456303198903	87	948	960	1030	2494	4128	6387	8850	10419	53405	729230
Subnet3772	17.5759931268305	87	760	948	960	1030	4128	5997	6387	8850	53405	729230
Subnet114	17.9897809431403	760	960	1030	5997	6387	7850	729230
...

Property file

...
100128640,-0.188755882547781
100128653,-0.469526295089429
100128727,-0.204911117918551
100128731,0.049874768167817
100128737,0.752653010432925
...

Output

<?xml version="1.0" encoding="utf-8" standalone="no"?>
<graphml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd" xmlns="http://graphml.graphdrawing.org/xmlns">
  <key attr.name="Pattern" attr.type="double" for="node" id="Pattern" xmlns="" />
  <key attr.name="T-Statistics" attr.type="double" for="node" id="T-Statistics" xmlns="" />
  <key attr.name="FoldChange" attr.type="double" for="node" id="FoldChange" xmlns="" />
  <key attr.name="Special" attr.type="double" for="node" id="Special" xmlns="" />
  <key attr.name="Count" attr.type="double" for="node" id="Count" xmlns="" />
  <graph edgedefault="undirected" id="Test" xmlns="">
    <node id="ACTN1">
      <data key="T-Statistics">15.9684277799701</data>
      <data key="FoldChange">-0.375438717117841</data>
      <data key="Special">0</data>
      <data key="Count">1</data>
    </node>
    <node id="CDKN2B">
      <data key="T-Statistics">-20.3132680459973</data>
      <data key="FoldChange">0.706842507345008</data>
      <data key="Special">0</data>
      <data key="Count">1</data>
    </node>
...

Last edited Feb 8, 2013 at 4:55 AM by yongkeecho, version 2

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