最近在系统学习clusterProfiler软件包，越用越觉得Y叔的强大，本节来介绍几个实用的小功能
k转ko
bitr_kegg可以对多个ko号进行转换此处传入字符向量即可
k <- c("K00799","K00844")
x <- bitr_kegg(k,"kegg","Path","ko")
> x
kegg Path
1 K00844 ko00010
2 K00844 ko00051
3 K00844 ko00052
4 K00799 ko00480
5 K00844 ko00500
6 K00844 ko00520
7 K00844 ko00521
翻译ko
y <- ko2name(x$Path)
ko name
1 ko00010 Glycolysis / Gluconeogenesis
2 ko00051 Fructose and mannose metabolism
3 ko00052 Galactose metabolism
4 ko00480 Glutathione metabolism
5 ko00500 Starch and sucrose metabolism
6 ko00520 Amino sugar and nucleotide sugar metabolism
left_join(x,y,by=c("Path"="ko"))
kegg Path name
1 K00844 ko00010 Glycolysis / Gluconeogenesis
2 K00844 ko00051 Fructose and mannose metabolism
3 K00844 ko00052 Galactose metabolism
4 K00799 ko00480 Glutathione metabolism
5 K00844 ko00500 Starch and sucrose metabolism
6 K00844 ko00520 Amino sugar and nucleotide sugar metabolism
7 K00844 ko00521 Streptomycin biosynthesis
8 K00844 ko00524 Neomycin, kanamycin and gentamicin biosynthesis
下载全部的k号对应的pathway信息
通过阅读clusterProfiler源代码发现有kegg_link此函数，源代码如下
## http://www.genome.jp/kegg/rest/keggapi.html
## kegg_link('hsa', 'pathway')
kegg_link <- function(target_db, source_db) {
url“ ”） <- paste0("http://rest.kegg.jp/link/", target_db, "/", source_db, collapse="")
kegg_rest(url)
}
clusterProfiler:::kegg_link("ko","pathway")
from to
1 path:map00010 ko:K00001
2 path:ko00010 ko:K00001
3 path:map00010 ko:K00002
4 path:ko00010 ko:K00002
5 path:map00010 ko:K00016
6 path:ko00010 ko:K00016
kegg_list <- function(db) {
url <- paste0("http://rest.kegg.jp/list/", db, collapse="")
kegg_rest(url)
}
clusterProfiler:::kegg_list("pathway")
clusterProfiler:::kegg_list("ko")
列出与人类相关的通路
clusterProfiler:::kegg_link("hsa","pathway")
from to
1 path:hsa00010 hsa:10327
2 path:hsa00010 hsa:124
3 path:hsa00010 hsa:125
4 path:hsa00010 hsa:126
5 path:hsa00010 hsa:127
6 path:hsa00010 hsa:128
ID转换
id <- c("4597","7111")
eg2np <- bitr_kegg(id,fromType='kegg',toType='ncbi-proteinid',organism='hsa')
kegg ncbi-proteinid
1 4597 NP_002452
2 7111 NP_001159588
np2up <- bitr_kegg(eg2np[,2], fromType='ncbi-proteinid',toType='uniprot',organism='hsa')
ncbi-proteinid uniprot
1 NP_002452 P53602
2 NP_001159588 P28289
参考：https://guangchuangyu.github.io/2016/05/convert-biological-id-with-kegg-api-using-clusterprofiler/
https://guangchuangyu.github.io/cn/2017/09/ko-id-conversion/
https://github.com/YuLab-SMU/clusterProfiler
