I have a question regarding the TOMType parameter in WGCNA blockWiseModule function.
I am interested in distinguishing positively and negatively correlated groups of genes, therefore I set networkType = "signed". By mistake, though, I put TOMType = "unsigned". Specifically:
net = blockwiseModules(data ,power= 6, TOMType ="unsigned", corType="pearson", networkType = "signed", minModuleSize = 30, reassignThreshold = 0, mergeCutHeight = 0.25, numericLabels = TRUE, pamRespectsDendro = FALSE,saveTOMs = T, verbose = 3)
I looked at the documentation but it still isn't clear to me what choosing TOMType = "unsigned" implies.
Additionally, I ran the function again changing to TOMType="signed" and the resulting modules seem to be very similar (almost all the same genes).
Is choosing NetworkType="signed" enough to retain the sign in the resulting modules?
Many thanks in advance for your help.