BuildGraph

Full name SMRUCC.genomics.Analysis.HTS.FELLA.Core.BuildGraph Assembly SMRUCC.genomics.Analysis.HTS.FELLA Members 3

Build KEGG graph from data sources.

In the R FELLA package, buildGraphFromKEGGREST() uses the KEGG REST API to download pathway, module, enzyme, reaction, and compound data. This VB.NET implementation provides:

File-based loading from tab-delimited text files
Programmatic graph construction
A built-in demo dataset for testing

01 Syntax

SMRUCC.genomics.Analysis.HTS.FELLA.Core.BuildGraph

02 Methods

Name	Overloads	Summary
BuildFromFiles	1	Build a KEGG graph from tab-delimited data files.
BuildDemoGraph	1	Build a demo KEGG graph for testing purposes.
BuildDataFromGraph	1	Build a FELLA data object from a KEGG graph.

03 Members

method BuildFromFiles #

BuildFromFiles(String, String)

Build a KEGG graph from tab-delimited data files.

Expected file format (tab-delimited, one entry per line):

nodes.txt: KEGG_ID NAME TYPE C00002 ATP compound R00100 reaction1 reaction ...

edges.txt: SOURCE_ID TARGET_ID EDGE_TYPE C00002 R00100 compound-reaction ...

method BuildDemoGraph #

BuildDemoGraph

Build a demo KEGG graph for testing purposes. This creates a small but realistic multi-layer graph that mimics the structure of a real KEGG metabolic network.

The demo graph contains:

3 pathways (Glycolysis, TCA Cycle, Purine Metabolism)
2 modules
5 enzymes
6 reactions
10 compounds

method BuildDataFromGraph #

BuildDataFromGraph(KeggGraph, Double, Double, Int32, Boolean, Boolean, Boolean)

Build a FELLA data object from a KEGG graph. This precomputes all matrices needed for enrichment analysis.