Hello,

I am interested in extracting information about the length of specific Reactome pathways (preferably using Bioconductor).

That is, given a pathway ID, I would like to know how many links it contains. Also, if possible, I would like to know how many links point to my Entity of interest, and how many links are there after it.

I am pretty new to bioinformatics and I hope I could make myself clear.

Thanks!

Hi vassialk,

I am interested in hoe many links and nodes a given pathway contains. This will be my measure of "length".

Just a hint: what you measure is usually called the pathway/network size (i.e., number of vertices, number of edges). Because pathways often have many connections (depends on the pathway and the database) and may contain circles, etc. some people prefer to use other metrics like the diameter.

Thank you very much for that info. Do you have any idea how I can calculate these parameters?

Yepp, check Wikipedia: calculate all shortest path between each pair of nodes (hint: Floyd's algorithm), then get the length of each shortest path, the maximum length is the diameter...

PS: I am quite confident, that there is already some graph package available on CRAN/BioConductor that implements the algorithm and/or diameter calculation.

So Reactome allows me to directly extract these informations (number of in-nodes, out-nodes, links, edges...) from the results they provide in R?

I don't know! I rarely use Reactome and have never used R for graph theory.

I just wanted to make you aware of the other graph/network metrics...