这个包依赖极有可能是这个：https://www.kegg.jp/kegg/docs/keggapi.html ，如果可以看懂会很好理解
由于KEGG数据库分享数据的策略改变，因此KEGG.db包不在能用，推荐KEGGREST包
But a number of years ago,KEGG changed their policy about sharing their data and so the KEGG.db package is no longer allowed to be current. Users who are interested in a more current pathway data are encouraged to look at the KEGGREST or reactome.db packages.
1、安装
if("KEGGREST" %in% rownames(installed.packages()) == FALSE) {source("http://bioconductor.org/biocLite.R");biocLite("KEGGREST")}
suppressMessages(library(KEGGREST))
ls('package:KEGGREST')
2、所有的对象及功能
keggConv：Convert KEGG identifiers to/from outside identifiers（ID转换功能）
keggFind：Finds entries with matching query keywords or other query data in a given database（即搜索功能）
keggGet：Retrieves given database entries（获取序列，图片等功能)
keggInfo：Displays the current statistics of a given database（即统计功能）
keggLink：Find related entries by using database cross-references（交互功能）.
keggList：Returns a list of entry identifiers and associated definition for a given database or a given set of database entries.
listDatabases：Lists the KEGG databases which may be searched.
mark.pathway.by.objects：Client-side interface to obtain an url for a KEGG pathway diagram with a given set of genes marked（标记功能）
3、每个对象的功能简单使用
3.1、keggConv（Convert KEGG identifiers to/from outside identifiers,即ID转换功能）
语法：keggConv(target, source, querySize = 100)
例子：
## conversion from NCBI GeneID to KEGG ID for E. coli genes##
head(keggConv("eco", "ncbi-geneid"),2)
head(keggConv("ncbi-geneid", "eco"),2)
########conversion from KEGG ID to NCBI GI##########
head(keggConv("ncbi-proteinid", c("hsa:10458", "ece:Z5100"))，2)
3.2）keggFind（Finds entries with matching query keywords or other query data in a given database，即检索功能）
语法：keggFind(database, query, option = c("formula", "exact_mass", "mol_weight"))
例子：
keggFind("genes", c("shiga", "toxin")) ## for keywords "shiga" and "toxin"
keggFind("genes", "shiga toxin") ## for keywords "shiga toxin"
keggFind("compound", "C7H10O5", "formula") ## for chemical formula "C7H10O5"
keggFind("compound", 174.05, "exact_mass") ## for 174.045 =< exact mass < 174.055
keggFind("compound", 300:310, "mol_weight") ## molecular weight 300 =< 310
3.3）keggGet (Retrieves given database entries,获取序列，图片等功能)
语法：keggGet(dbentries, option = c("aaseq", "ntseq", "mol", "kcf","image", "kgml"))
keggGet(c("cpd:C01290", "gl:G00092")) ## retrieves a compound entry and a glycan entry
keggGet(c("C01290", "G00092")) ## same as above, without prefixes
keggGet(c("hsa:10458", "ece:Z5100")) ## 检索 a human gene entry and an E.coli O157 gene entry
keggGet(c("hsa:10458", "ece:Z5100"), "aaseq") ## 检索 amino acid sequences of a human gene and an E.coli O157 gene
png <- keggGet("hsa05130", "image") ## retrieves the image file of a pathway map
t <- 'hsa05130.png'
library(png)
writePNG(png, t)
keggGet("hsa05130", "kgml")
hsa05130.png
3.4）keggInfo（Displays the current statistics of a given database,即统计功能）
语法:keggInfo(database)
head(keggInfo("kegg") ## displays the current statistics of the KEGG database
keggInfo("pathway") ## displays the number pathway entries including both the reference and organism-specific pathways
keggInfo("hsa") ##### displays the number of gene entries for the KEGG organism Homo sapiens
3.5）keggLink（keggLink Find related entries by using database cross-references.交互功能）
语法：keggLink(target, source)
head(keggLink("pathway", "hsa")，5) ### KEGG pathways linked from each of the human genes
head(keggLink("hsa", "pathway")，5) ## human genes linked from each of the KEGG pathways
head(keggLink("pathway", c("hsa:10458", "ece:Z5100")),5) ## KEGG pathways linked from a human gene and an E. coli O157 gene
head(keggLink("hsa:126"),5)
3.6) keggList (Returns a list of entry identifiers and associated definition for a given database or set of database entries，返回信息表)
用法：keggList(database, organism)
keggList("pathway") ## returns the list of reference pathways
keggList("pathway", "hsa") ## returns the list of human pathways
keggList("organism") ## returns the list of KEGG organisms with taxonomic classification
keggList("hsa") ## returns the entire list of human genes
keggList("T01001") ## same as above
keggList(c("hsa:10458", "ece:Z5100")) ## returns the list of a human gene and an E.coli O157 gene
keggList(c("cpd:C01290","gl:G00092")) ## returns the list of a compound entry and a glycan entry
keggList(c("C01290+G00092")) ## same as above (prefixes are not necessary)
3.7） listDatabases（Lists the KEGG databases which may be searched.查看有数据库）
用法：listDatabases()
例子：
listDatabases() ##查看有哪些数据库
3.8）mark.pathway.by.objects：Client-side interface to obtain an url for a KEGG pathway diagram with a given set of genes marked（标记功能，例如上调y用红框，下调用绿框）
语法：
mark.pathway.by.objects(pathway.id, object.id.list)
color.pathway.by.objects(pathway.id, object.id.list,fg.color.list, bg.color.list)
例子：
url <- mark.pathway.by.objects("path:eco00260",c("eco:b0002", "eco:c00263"))
if(interactive()){browseURL(url)}
url <- color.pathway.by.objects("path:eco00260",c("eco:b0002", "eco:c00263"),c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))
