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Question: How to calculate the shortest path between each pairs of genes in WGCNA
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gravatar for Ati
12 months ago by
Ati • 30
Ati • 30 wrote:

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

R gene co-expression analysis wgcna • 402 views
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modified 12 months ago by Benn ♦ 7.9k • written 12 months ago by Ati • 30
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gravatar for geek_y
12 months ago by
geek_y ♦ 10k
Barcelona
geek_y ♦ 10k 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 COMMENT • link written 12 months ago by geek_y ♦ 10k

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

ADD REPLY • link written 12 months ago by Ati • 30

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

ADD REPLY • link written 12 months ago by geek_y ♦ 10k
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