Use simplify to remove redundant terms in enrichGO

[jinshengheshi]

ego2 <- simplify(ego_0.05, cutoff = 0.7, by = "p.adjust", select_fun = min) Error in simplify(ego_0.05, cutoff = 0.7, by = "p.adjust", select_fun = min) : 参数没有用(cutoff = 0.7, by = "p.adjust", select_fun = min)

Hello，how could I fix the problem? My package version is 4.2.2. Gratefully appreciate.

[zhangyz1997]

I have tried to use simplify for gseGO results

clusterProfiler::simplify(gseGO( geneList = gene_list_new, OrgDb = org.Hs.eg.db, ont = "ALL", minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05, verbose = TRUE ))

However it returns

preparing geneSet collections... GSEA analysis... leading edge analysis... done... Error in .local(x, ...) : simplify only applied to output from gseGO and enrichGO...

[jinshengheshi]

Y神，您好，我按照论坛上的建议，从 github 上安装了Clusterprofiler，版本是4.3.4，但还是一样的问题……
请问我想用simplify包的话，应该怎么解决报错呢？ （附件是 ego_0.05 的富集结果）
耽误您宝贵的时间了，十分感谢🙏🙏🙏

2022年4月21日 19:07，zhangyz1997 @.***> 写道：

I have tried to use simplify for gseGO results

clusterProfiler::simplify(gseGO( geneList = gene_list_new, OrgDb = org.Hs.eg.db, ont = "ALL", minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05, verbose = TRUE ))

However it returns

preparing geneSet collections... GSEA analysis... leading edge analysis... done... Error in .local(x, ...) : simplify only applied to output from gseGO and enrichGO...

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[huerqiang]

@jinshengheshi 是不同R包的同名函数问题，使用clusterProfiler::simplify来指定。

[huerqiang]

@zhangyz1997 Use the latest version of clusterProfiler.