org.Hs.eg.db 使用 clusterProfiler 的问题

Question

有谁知道为什么这不起作用？调用 org.Hs.eg.db.

时出错

ego <- enrichGO(gene          = gene.df,
                universe      = names(geneList),
                OrgDb         = org.Hs.eg.db,
                ont           = "CC",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.01,
                qvalueCutoff  = 0.05,
                readable      = TRUE)

   > head(geneList)
          ENSEMBL ENTREZID   SYMBOL
1 ENSG00000000419     8813     DPM1
2 ENSG00000000457    57147    SCYL3
3 ENSG00000000460    55732 C1orf112
4 ENSG00000000971     3075      CFH
5 ENSG00000001036     2519    FUCA2
6 ENSG00000001084     2729     GCLC

> head(gene.df)
          ENSEMBL ENTREZID SYMBOL
1 ENSG00000100427    23209   MLC1
2 ENSG00000008517     9235   IL32
3 ENSG00000081237     5788  PTPRC
4 ENSG00000162645     2634   GBP2
5 ENSG00000000971     3075    CFH
6 ENSG00000115415     6772  STAT1

Error in enrichGO(gene = gene.df, universe = names(geneList), OrgDb = org.Hs.eg.db,  : 
  unused argument (OrgDb = org.Hs.eg.db)

Answer 1

尝试指向数据框的 entrez 列。

例如：

ego <- enrichGO(gene          = gene.df$ENTREZID,
                universe      = geneList$ENTREZID,
                OrgDb         = org.Hs.eg.db,
                ont           = "CC",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.01,
                qvalueCutoff  = 0.05,
                readable      = TRUE)

Answer 2

问题是 RStudio 中的旧版本 R。

org.Hs.eg.db 使用 clusterProfiler 的问题

Problems with org.Hs.eg.db using clusterProfiler

r

ontology

bioinformatics

bioconductor