[BioC] topGO desperation

[Oertlin, Christian (Stud. FHML)]

Hey Jim,

well I guess the problem lies somewhere in how the file is built up. But I cannot find how it should be.

setwd("/Users/christianoertlin/Desktop/Stage files/R")
read.csv("first.csv", header=TRUE, sep=",")
library(topGO)
read.table("first.csv",header=TRUE,sep=",")
resultFisher <- runTest("first.csv", algrotithm="classic",statistic="Fisher")
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘runTest’ for signature ‘"character", "missing", "character"’

This is my problem. The fisher test does not recognize my file as something to work with. I tried moving some rows in the file but it did not work either. Tbh I have no clue what is wrong with it. I added the file in the mail.

The file is an output generated by GO-elite. I already have my GO term with an outcome I just want to do some test and map them into a graph. Like it is done with the from the topGO example.

showSigOfNodes(GOdata, score(resultKS.elim), firstSigNodes = 5, useInfo = 'all')

Kind Regards,
Christian