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

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

wgcna r gene co-expression analysis

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updated 7.5 years ago by Benn

• written 7.5 years ago by Ati •

1 answer

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

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written 7.5 years ago by GouthamAtla

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

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written 7.5 years ago by Ati •

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

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written 7.5 years ago by GouthamAtla

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