Question: How to calculate the shortest path between each pairs of genes in WGCNA
0
gravatar for Ati
12 months ago by
Ati30
Ati30 wrote:

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

ADD COMMENTlink modified 12 months ago by Benn7.9k • written 12 months ago by Ati30
0
gravatar for geek_y
12 months ago by
geek_y10k
Barcelona
geek_y10k wrote:

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

ADD COMMENTlink written 12 months ago by geek_y10k

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

ADD REPLYlink written 12 months ago by Ati30

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

ADD REPLYlink written 12 months ago by geek_y10k
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