Closed NancyKelly1224 closed 1 year ago
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?
KEGG.db
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
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。
还是更了,https://github.com/YuLab-SMU/createKEGGdb/pull/8.
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: