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[igraph] Help combining vertices with the same ID into one new vertex an

From: Alex Upton
Subject: [igraph] Help combining vertices with the same ID into one new vertex and removing multiple edges resulting from this
Date: Wed, 19 Sep 2012 03:27:43 +0100

Good evening,

I am having some trouble with something. I have a dataset, which contains probe 
IDs and gene symbols. After creating a weighted igraph with the probe IDs as 
the vertex names, I then map them to the gene symbols. 

This is the code for what I have done:

V(gone)$gene_ID =as.character(annot$Sym[match(V(gone)$name,annot$probeset_id)]) 
# map the probe IDs to gene symbols

V(gone)$gene_ID # returns the list of gene symbols, with multiples vertices 
having the same gene symbol, i.e. not all unique entries

The issue is that for some gene symbols, multiples probes map to just one gene 
symbol. Therefore, what I would like to do is use V(gone)$gene_ID to create a 
new graph with only unique vertex values for this attribute. This would result 
in fewer vertices. Then, if possible, I would like to remove the mutliple edges 
that would exist as a result of this, and keep just the highest weighted edge 
between two vertices, instead of the multiple ones that may now exist. Any help 
with this would be greatly appreciated as I have tried different approaches so 
far, and none of them have worked.

Kind regards,


Alex Upton, BEng, MRes, PG Cert Business Administration

PhD Researcher Biomedical Informatics, Signals and Systems 
School of Electronic, Electrical and Computer Engineering, 
College of Engineering and Physical Sciences, University of Birmingham
Edgbaston, Birmingham, B15 2TT, United Kingdom

Fax: +44 121 4144291 (school general office)
Email: address@hidden

Personal Web: http://postgrad.eee.bham.ac.uk/uptona/

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