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

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.

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.