kegg富集分析之：KEGGREST包（9大功能）

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"))