Entering edit mode
8.3 years ago
zizigolu
★
4.3k
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
Note that my answer means you should use:
not
thank you I used
but no happen I saw
I know you won't get any output from that, but if you
head()
the file orView()
it or whatever then it should be correct.thank you,
may you please help me to remove gene-gene interaction from my matrix?
What I wrote will presumably set those to 0. There's no way to actually remove them from the matrix.
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
is only a value equal to 0 and not re writable or Viewable
That changes
Net
. JustView(Net)
. If you want that as a different object thensorry but
somethingNew <- Net
is the same
while I need the result of
as a different object
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.
ok thank you