Search
Question: WGCNA cytoscape export question
0
gravatar for akridgerunner
3.2 years ago by
United States
akridgerunner10 wrote:

Hi,

We've successfully exported the top hub genes in a module to Cytoscape from a network based on a single TOM. However, how do export from networks based on multiple TOMs? Do the TOMs have to be merged somehow, and if so, do you have a script snippet?

Thanks as always,

Robert

ADD COMMENTlink modified 3.2 years ago by Peter Langfelder1.5k • written 3.2 years ago by akridgerunner10
1
gravatar for Peter Langfelder
3.2 years ago by
United States
Peter Langfelder1.5k wrote:

There is only one TOM for the entire network. The module TOM you reference is (if I understand your question right) the full network TOM subset to the module genes. You can subset the TOM to any subset of genes you like, for example hubs from different modules, or all genes from several modules.

ADD COMMENTlink written 3.2 years ago by Peter Langfelder1.5k

Hi Peter, I had to set my maxblocksize to 20,000 so I got three TOMs during network creation, so I'm not sure how to handle this. Thanks again.

ADD REPLYlink written 3.2 years ago by akridgerunner10
1
gravatar for Peter Langfelder
3.2 years ago by
United States
Peter Langfelder1.5k wrote:

The silent assumption in blockwise analysis is that TOM between genes in different blocks is zero, so you could also use this assumption. See the help for blockwiseModules, especially the output component blockGenes which tells you which genes went into each block.

The alternative, if you are patient, is to use the function vectorTOM. This allows you to calculate TOM among a subset of genes/probes as long as the subset is not too large. You need patience because the function is slower than standard TOM calculation, but will give you TOM among the subset of genes.
 

ADD COMMENTlink written 3.2 years ago by Peter Langfelder1.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 309 users visited in the last hour