clusterProfiler update KEGG.db
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@happylittlepig-11095
Last seen 7.8 years ago

the clusterProfiler version is 3.0.4,here are the errors i met  when i use this pakage in Rstudio. Thank you for your answers and this will help many people who use this pakage.

1.Error about use_internal_data=FALSE 

library(clusterProfiler)
library("DOSE")
data(geneList)
gene <- names(geneList)[abs(geneList) > 2]
head(gene)
#[1] "4312"  "8318"  "10874" "55143" "55388" "991"  
kk <- enrichKEGG(gene         = gene,
  organism     = "human",
  pvalueCutoff = 0.05,
  readable     = TRUE,
  use_internal_data = FALSE)
Error in `$<-.data.frame`(`*tmp*`, "Description", value = c("Glycolysis / Gluconeogenesis",  : 
  替换数据里有169行,但数据有0

2. function download.KEGG() doesn't exist

download.KEGG()
Error: could not find function "download.KEGG"

 

software error download.kegg() kegg.db use_internal_data = FALSE • 1.4k views
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Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 26 days ago
China/Guangzhou/Southern Medical Univer…

first of all, you should tag your post with the package name, clusterProfiler. Only in this way, I can receive email notification.

 

kk <- enrichKEGG(gene         = gene,
  organism     = "human",
  pvalueCutoff = 0.05,
  readable     = TRUE,
  use_internal_data = FALSE)

 

If you run this code, you should get the following error:

Error in enrichKEGG(gene = gene, organism = "human", pvalueCutoff = 0.05,  :
  unused argument (readable = TRUE)

since there is no readable argument for enrichKEGG.

I run your code without the readable argument, it works fine and gives the following result:

> head(summary(kk))
               ID                             Description GeneRatio  BgRatio
hsa04110 hsa04110                              Cell cycle     11/84 124/7081
hsa04114 hsa04114                          Oocyte meiosis     10/84 123/7081
hsa03320 hsa03320                  PPAR signaling pathway      7/84  72/7081
hsa04914 hsa04914 Progesterone-mediated oocyte maturation      6/84  98/7081
hsa04115 hsa04115                   p53 signaling pathway      5/84  69/7081
hsa04062 hsa04062             Chemokine signaling pathway      8/84 187/7081
               pvalue     p.adjust       qvalue
hsa04110 1.915578e-07 3.218171e-05 3.165745e-05
hsa04114 1.616186e-06 1.357596e-04 1.335480e-04
hsa03320 2.029899e-05 1.136744e-03 1.118225e-03
hsa04914 1.026096e-03 4.309603e-02 4.239396e-02
hsa04115 1.291558e-03 4.339635e-02 4.268939e-02
hsa04062 1.598654e-03 4.476231e-02 4.403310e-02
                                                     geneID Count
hsa04110 8318/991/9133/890/983/4085/7272/1111/891/4174/9232    11
hsa04114    991/9133/983/4085/51806/6790/891/9232/3708/5241    10
hsa03320                 4312/9415/9370/5105/2167/3158/5346     7
hsa04914                         9133/890/983/4085/891/5241     6
hsa04115                             9133/6241/983/1111/891     5
hsa04062           3627/10563/6373/4283/6362/6355/9547/1524     8

 

For the second issue, the function is not exported.

 

 

 

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