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 -------------------------------------------------------------------------------------------- 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: [email protected] Personal Web: http://postgrad.eee.bham.ac.uk/uptona/ -------------------------------------------------------------------------------------------- _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
