I wanted to share my issue with WGCNA. any help would be very valuable for me
I wanted to know that for identifying modules related with Stage I to Stage IV, how can i binarize these stages into 0, 1, 2, 3, respectively? i have to to this on excel as below:
and then in the bellow code?how to change it?
library(WGCNA) x = rep(c("stage_I", "stage_II", "stage_III", "stage_IV"), each = 4) # Binarize it into pairwise indicators out = binarizeCategoricalVariable(x, includePairwise = TRUE, includeLevelVsAll = FALSE); # Print the variable and the indicators data.frame(x, out);
And is this a good idea? before seeing your good suggestion i wanted to separately analyze per-proccessed DEGs from TCGAbiolink with WGCNA, but for TCGA-COADREAD, 4 different analysis for stages is required, and this is a bad idea.