Get NA Description

[NancyKelly1224]

Y叔好，

我用KEGG数据本地化，再也不用担心网络问题了提供的代码安装了KEGG.db，运行示例代码的时候发现结果的Description列是NA，我注意到clusterProfiler更新了KEGG的API， 是不是KEGG API改变导致的这个问题呢？

代码和结果如下：

# 本地化
remotes::install_github("YuLab-SMU/createKEGGdb")
createKEGGdb::create_kegg_db("hsa")
install.packages("./KEGG.db_1.0.tar.gz",repos=NULL)

# 使用
data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]

kk <- clusterProfiler::enrichKEGG(gene = gene,
                 organism     = 'hsa',
                 pvalueCutoff = 0.05,
                 qvalueCutoff = 0.05,
                 use_internal_data =T)
kk
#
# over-representation test
#
#...@organism    hsa 
#...@ontology    KEGG 
#...@keytype     kegg 
#...@gene    chr [1:207] "4312" "8318" "10874" "55143" "55388" "991" "6280" "2305" "9493" "1062" "3868" "4605" "9833" ...
#...pvalues adjusted by 'BH' with cutoff <0.05 
#...9 enriched terms found
'data.frame':   9 obs. of  9 variables:
 $ ID         : chr  "hsa04110" "hsa04114" "hsa04218" "hsa04061" ...
 $ Description: chr  NA NA NA NA ...
 $ GeneRatio  : chr  "11/94" "10/94" "10/94" "8/94" ...
 $ BgRatio    : chr  "127/8275" "131/8275" "156/8275" "100/8275" ...
 $ pvalue     : num  1.69e-07 2.05e-06 9.88e-06 1.62e-05 2.06e-05 ...
 $ p.adjust   : num  3.53e-05 2.14e-04 6.88e-04 8.48e-04 8.62e-04 ...
 $ qvalue     : num  3.45e-05 2.09e-04 6.72e-04 8.28e-04 8.42e-04 ...
 $ geneID     : chr  "8318/991/9133/890/983/4085/7272/1111/891/4174/9232" "991/9133/983/4085/51806/6790/891/9232/3708/5241" "2305/4605/9133/890/983/51806/1111/891/776/3708" "3627/10563/6373/4283/6362/6355/9547/1524" ...
 $ Count      : int  11 10 10 8 7 7 5 8 10
#...Citation
  Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
  clusterProfiler: an R package for comparing biological themes among
  gene clusters. OMICS: A Journal of Integrative Biology
  2012, 16(5):284-287 

[GuangchuangYu]

这种方式已经没有再维护了，你到YuLabSMU公众号上搜索gson，能够获得当前更好的支持。

[GuangchuangYu]

还是更了，https://github.com/YuLab-SMU/createKEGGdb/pull/8.