How to calculate the shortest path between each pairs of genes in WGCNA

Question

[Ati]

I would like to have the shortest path or distance between different pairs of genes in a network constructed by WGCNA R package.

Answer 1

[GouthamAtla]

If you want to do it in python, https://networkx.github.io check Shortest Paths

If you want to do it in R, https://igraph.org/redirect.html check shortest.paths

[Ati]

Thanks for the reply. Then which output should be used (Adjacency, TOM or dissTOM)?

[GouthamAtla]

You have to use one of the export network functions to get the network from WGCNA.