Hi,

I have a complete list of transcription factors in Arabidopsis thaliana like below

TF <- read.table("whole TF.txt", header = T, sep = "\t")

> View(TF)

AGI_ID
AT1G01010
AT1G01030
AT1G01060
AT1G01160
AT1G01210
AT1G01250

and and by my expression data sets I produced a correlation matrix contains both genes and transcription factors like below

>genes <- read.table("genes.txt", header = T, sep = "\t")
> library(netbenchmark)
> Net <- cor(genes)
> head(Net[1:4,1:4])

            AT1G01060   AT1G01170   AT1G01260   AT1G01380
AT1G01060  1.00000000  0.34783519 -0.09805551 -0.17400162
AT1G01170  0.34783519  1.00000000 -0.47605524  0.04211973
AT1G01260 -0.09805551 -0.47605524  1.00000000 -0.04742131
AT1G01380 -0.17400162  0.04211973 -0.04742131  1.00000000

In the above matrix I have interaction between gene-gene, gene-transcription factor and transcription factor-transcription factor. I want to remove gene-gene part from above matrix by setdiff function.

I did like below

nonTF <- setdiff(Net, TF)
Net <- Net[nonTF,nonTF]==0

But View(Net) is FALSE

and

Net <- Net[nonTF, nonTF] <- 0

View(Net) is 0

Then how can I remove gene-gene interaction from my correlation matrix and keep the rest of interactions please?

Thank you