Question: genie3 package Error in (function (classes, fdef, mtable)
1
gravatar for Sam
2.1 years ago by
Sam140
Sam140 wrote:

Dear All

I have problem with genie3 package(inferring gene regulatory networks from expression data). Any idea why i am getting this error?

> head(test2)
      Sample1 Sample2 Sample3 Sample4 Sample5
Gene1       1       5       9       5       2
Gene2       3       7       7       2       2
Gene3       6       3       7       8      10
Gene4       5       1       9       9       4
Gene5       9      10       7       7       4
Gene6       3       4       9       5       7
> set.seed(123)
> weightMat <- GENIE3(test2)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘GENIE3’ for signature ‘"data.frame"’
R genie3 • 1.3k views
ADD COMMENTlink modified 2.1 years ago by Ram32k • written 2.1 years ago by Sam140
2
gravatar for Ram
2.1 years ago by
Ram32k
Baylor College of Medicine, Houston, TX
Ram32k wrote:

In my experience, this error happens when one tries to use an incompatible input type as an input parameter to a function as called from the current session with its loaded Namespaces. Given that GENIE3() is most probably not a function masked by a different namespace, it's probably just that the first parameter being passed to GENIE3() is of an invalid type.

From the manual, GENIE3() is described to accept a matrix, not a data.frame, which is what test2 is. Try using as.matrix(test2) as the input, that might work. You should also try Googling the error message and reading the manual carefully, as most error messages make the problem clear.

P.S.: To understand the "as called from the current session with its loaded Namespaces" part (the phenomenon called "namespace conflicts"), please see this StackOverflow answer.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Ram32k
2
gravatar for Santosh Anand
2.1 years ago by
Santosh Anand5.3k
Santosh Anand5.3k wrote:

I guess you need a matrix, whereas you are passing a data.frame. Try

GENIE3(as.matrix(test2))
ADD COMMENTlink written 2.1 years ago by Santosh Anand5.3k

Thanks a lot, it worked

ADD REPLYlink written 2.1 years ago by Sam140
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