如何构建自己的KEGG数据库

本文转自Y叔公众号

自己KEGG数据库好处：

1. 可重复性好
2. 没网也可以进行分析

步骤

1 在KEGG官网找到自己物种的3字符缩写

2 加载Y叔获取kegg.db 的R包

1 ##安装Y叔的包
2 library(remotes)
remotes::install_github("YuLab-SMU/createKEGGdb")
#若报错 force ,则强制安装
remotes::install_github("YuLab-SMU/createKEGGdb", force = TRUE)
  checking for file ‘/private/var/folders/yc/9wjshngs31513v_mw3tkxgs00000gn/T/RtmpnuOrB5/remotesefd0472c4df1/YuLab-SMU-createKEGGdb-378e7cf/DESCRIPTION’ (421ms)
─  preparing ‘createKEGGdb’:
  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘createKEGGdb_0.0.2.tar.gz’

* installing *source* package ‘createKEGGdb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (createKEGGdb)

3 下载所需要物种的KEGG.db

## 下载所需要物种的KEGG.db
createKEGGdb::create_kegg_db('soe')
019-12-27 15:13:29 Getting KEGG data of soe.
2019-12-27 15:13:29 KEGG data of soe has been downloaded.
2019-12-27 15:13:29 KEGG data of soe has been added to the sqlite database.
  checking for file ‘/private/var/folders/yc/9wjshngs31513v_mw3tkxgs00000gn/T/RtmpnuOrB5/fileefd0bae49ad/DESCRIPTION’ (463ms)
─  preparing ‘KEGG.db’:
  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘KEGG.db_1.0.tar.gz’

 "./KEGG.db_1.0.tar.gz"

## 安装下载好的KEGG.db 包
install.packages("KEGG.db_1.0.tar.gz",repos=NULL, type = "source")
* installing *source* package ‘KEGG.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘KEGG.db’
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (KEGG.db)

4 测试本地的包

 1 library(KEGG.db)
 2 library(clusterProfiler)
 3
 4 ## 加载基因名字，ENTREZID格式
 5 gene = read.table("geneList.blastp_filter_ENTREZID",sep = "\t",header = T)
 6 gene = as.character(gene$Name)
 7 head(gene)
 8 [1] "110778909" "110805947" "110782171" "110800757" "110785314" "110789473"
 9 kegg <- enrichKEGG(gene = gene,
10                    organism = 'soe',
11                    pvalueCutoff = 0.05,
12                    qvalueCutoff = 0.05,
13                    use_internal_data = T)
14
15 cnetplot(kegg)

结束！