I am following the WGCNA tutorial on my own dataset, but I am currently stuck in section 5.
Specifically in the first section of the guide.
# Calculate topological overlap anew: this could be done more efficiently by saving the TOM # calculated during module detection, but let us do it again here. dissTOM = 1-TOMsimilarityFromExpr(datExpr, power = 6); # Transform dissTOM with a power to make moderately strong connections more visible in the heatmap plotTOM = dissTOM^7; # Set diagonal to NA for a nicer plot diag(plotTOM) = NA; # Call the plot function sizeGrWindow(9,9) TOMplot(plotTOM, geneTree, moduleColors, main = "Network heatmap plot, all genes")
I am trying to calculate dissTOM, but since my dataset is too large I calculated the modules in a block wise manner, described in section 2c.
To calculate TOM, the function appears to re-calculate adjacency. The guide itself states this will not work for modules calculated blockwise, but I am not sure how to modify the code to fit my data. How do I recalculate TOM if I used the block wise approach to create my network?