售后

原因：通路中gene名字与注释文件（kegg.xls）gene名字不匹配

报错代码

Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [rest.kegg.jp] Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
Info: Getting gene ID data from KEGG...
Info: Done with data retrieval!
Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.

解决办法

1.重新下载通路图，下载代码如下

/TJPROJ6/RNA_SH/script_dir/KEGG/get_kegg_html.py --get all --type net --abbr aly（物种三字母缩写） --out 下载路径/aly

2.将富集流程中 –keggdir 参数填写为 下载路径/aly ，–keggdb 参数填写为 下载路径 ，重新跑出通路图的代码即可。