Question: How to calculate the shortest path between each pairs of genes in WGCNA
0
gravatar for abc
11 weeks ago by
abc30
abc30 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 11 weeks ago by Benn6.6k • written 11 weeks ago by abc30
0
gravatar for geek_y
11 weeks ago by
geek_y9.4k
Barcelona/CRG/London/Imperial
geek_y9.4k 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 11 weeks ago by geek_y9.4k

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

ADD REPLYlink written 11 weeks ago by abc30

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

ADD REPLYlink written 11 weeks ago by geek_y9.4k
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