3.2 years ago by
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.