Question: WGCNA::cor namespace issue
0
gravatar for arjunsbaghela
9 days ago by
arjunsbaghela10 wrote:

Hello,

I am getting this error when running WGCNA's blockwiseModules function:

Error in (new("standardGeneric", .Data = function (x, y = NULL, use = "everything", : unused arguments (weights.x = NULL, weights.y = NULL, cosine = FALSE)

I am pretty sure the problem is that the stats::cor function is being used under the hood, rather than WGCNA::cor. I have not found a fix to this issue and it seems many people are experiencing it. Can anyone recommend a workaround.

I have tried loading WGCNA package last, but this does not work either.

Thanks, Arjun

cor wgcna • 109 views
ADD COMMENTlink modified 9 days ago • written 9 days ago by arjunsbaghela10

Yes, this issue has been reported before: Error in (function...) thrown by WGCNA tutorial (R)

As mentioned, it's some namespace issue. I had suggested that the cor function that WGCNA wants to use is now outdated, which causes some conflict. WGCNA is not really maintained anymore. Please see if you can find the answer in the other thread to which I have linked you.

ADD REPLYlink written 9 days ago by Kevin Blighe24k
0
gravatar for arjunsbaghela
9 days ago by
arjunsbaghela10 wrote:

I think I found a solution when working in RStudio... from the "Session" pulldown, press restart R.

Then run library(WGCNA).

Run search(): ".GlobalEnv", "package:WGCNA" should be the first and second characters in the vector.

Then run the blockwiseModules function.

Hope this works for other people.

Arjun

ADD COMMENTlink modified 9 days ago • written 9 days ago by arjunsbaghela10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 657 users visited in the last hour