removing gene-gene interaction from a correlation matrix

Question

[zizigolu]

Hi,

I have a list of transcription factors like below

TF <- read.table("whole TF.txt", header = T, sep = "\t")
> View(TF)
AGI_ID
AT1G01010
AT1G01030
AT1G01060
AT1G01160
AT1G01210
AT1G01250

and 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

Then how I can remove gene-gene interaction from my correlation matrix please?

Thank you

[Devon Ryan]

Note that my answer means you should use:

Net[nonTF, nonTF] <- 0

not

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

[zizigolu]

thank you I used

Net[nonTF, nonTF] <- 0

but no happen I saw

[Devon Ryan]

I know you won't get any output from that, but if you head() the file or View() it or whatever then it should be correct.

[zizigolu]

thank you,

may you please help me to remove gene-gene interaction from my matrix?

[Devon Ryan]

What I wrote will presumably set those to 0. There's no way to actually remove them from the matrix.

[zizigolu]

thank you I think I got your mean. you made those interaction 0. now how I can extract the resulted matrix (the matrix with gene-gene interaction=0) ??? because the result of

Net[nonTF, nonTF] <- 0

is only a value equal to 0 and not re writable or Viewable

[Devon Ryan]

That changes Net. Just View(Net). If you want that as a different object then

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

[zizigolu]

sorry but

somethingNew <- Net

is the same

Net <- cor(genes)

while I need the result of

Net[nonTF, nonTF] <- 0

as a different object

[Devon Ryan]

I know, I showed you EXACTLY how to do that. Read what I wrote. There is no reason to ask any further questions about this, you've already received all the answers you need.

[zizigolu]

ok thank you

Answer 1

[Devon Ryan]

You presumably meant Net[nonTF, nonTF] <- 0 as the last line...