genie3 package Error in (function (classes, fdef, mtable)

Question

[Sam]

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"’

Answer 1

[Ram]

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.

Answer 2

[Santosh Anand]

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

GENIE3(as.matrix(test2))

[Sam]

Thanks a lot, it worked