Hi everyone!
I am absolutely new to R but I need to construct gene networks based on co-expression. The problem is that I only want to look at the genes that are co-expressed with one single gene of interest across different RNA-seq datasets from tumors. I've read through the tutorials but realized that this package is usually used for exploring networks of all the genes present in the datasets. Is there a way to just focus on one particular gene of interest as the 'hub gene' already from the begining? Or is there any other software/program that can serve this purpose better?
(sorry if this sounds ignorant but any help would be appreciated!)
Iris
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written
by
iriswt •
1 answer
You likely are referring to the 'first nearest neighbours' [of a node/vertex]. In WGCNA, you can use this function: nearestNeighborConnectivity.
As you imply, checking the vertex hub score can help too. Other metrics include
- vertex degree
- betweenness centrality
- closeness centrality
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