unused argument (organism="human")
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zhaoxiao • 0
@zhaoxiao-11480
Last seen 7.5 years ago

     I have installed the R (R version 3.3.1) package of clusterProfile and run it step by step on the basis of Mr Yu's work "Using clusterProfiler to identify and compare functional profiles of gene lists ".It's strange that it occured an error described below:

> library(clusterProfiler)

Loading required package: DOSE

> require(DOSE)

> data(geneList)

> gene <- names(geneList)[abs(geneList) > 2]

ggo <- groupGO(gene = gene, organism = "human", ont = "BP",level = 3, readable = TRUE)

Error in groupGO(gene = gene, organism = "human", ont = "BP", level = 3,  : 

unused argument (organism = "human")

   I don't understand why there should be an error like that and ask all of you for suggestions. Thanks.

 

error • 2.2k views
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li lilingdu ▴ 450
@li-lilingdu-1884
Last seen 5.9 years ago

Your document might be obsolete. you can install the latest clusterProfiler package, and look at the help info for function groupGO where the 2nd parameter should be  OrgDb (the meta package name)

groupGO(gene, OrgDb, keytype = "ENTREZID", ont = "CC", level = 2,
  readable = FALSE)
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Thanks for your advices,li lilingdu.And I surely made a low-level mistake that I have installed the latest clusterProfiler package while referring to the old functional documentation.

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