Question

晚上好，
我有一个奇怪的问题。
首先，我向您展示了我使用的工具。可能有解决方案，但我不确定

library(clusterProfiler)
library(pathview)
library(DOSE)
library(org.Hs.eg.db)

我正在尝试进行常规的GO分类。因此，我使用了http://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

中的示例命令

genenamesSymbol$ab<-c("IFI6","IFNL2","EGR3","FHL3","TNFAIP3","SERTAD2","NR4A3","AKR1C8P","NEK6","TMEM177","CERK","ZNF713","IKZF3","F3","TUBA8","GPNMB","SALL3","SDCCAG3","HIST2H3A","SHANK2","FUNDC2","FAM195A","GPR87","ENO1","LILRA5","NXT1","TRPM2","STX18","ENTHD2","ASPM","RHOV","HIST1H3D","PSTK","NUDT15","ENPEP","TRMU","ZDHHC23","ACAP2","CCL25","ATL3","ADPRM","KRTAP5-11")

只是一些随机基因的例子

genenames.data.frame <- bitr(genenamesSymbol$ab, fromType = "SYMBOL",
                         toType = c("ENTREZID"),
                         OrgDb = org.Hs.eg.db)
gene <- genenames.data.frame[,2]
ggo <- groupGO(gene     = gene,
           OrgDb    = org.Hs.eg.db,
           ont      = "BP",
           level    = 3,
           readable = TRUE)
head(ggo)
barplot(ggo, drop=TRUE, showCategory=12)

普通头（ggo）应该显示如下内容。

                   ID                    Description Count GeneRatio
## GO:0005886 GO:0005886                plasma membrane    54    54/207
## GO:0005628 GO:0005628              prospore membrane     0     0/207
## GO:0005789 GO:0005789 endoplasmic reticulum membrane     8     8/207

对我来说，它显示一个空表。

[1] ID          Description Count       GeneRatio   geneID     
<0 rows> (or 0-length row.names)

通常我希望为GroupGO提供正确的基因列表会出错，或者基因列表本身为空。但是，当我用ggo做一个barplot时，会显示一些结果。所以ggo不能为空。
我对此问题感到困惑。

不幸的是，这对于我的学士学位论文很重要。这就是为什么我希望有人对我有解决方案。

感谢您的帮助或建议，
朱利安

ClusterProfiler头（GroupGO）什么都不显示

0 个答案: