WGCNA for diferent stages (I-IV)

WGCNA for diferent stages (I-IV)


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:

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and then in the bellow code?how to change it?

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.

thank you




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