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
1 2 3 | 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##
1 | head ( keggConv ( "eco" , "ncbi-geneid" ),2) |
1 | head ( keggConv ( "ncbi-geneid" , "eco" ),2) |
########conversion from KEGG ID to NCBI GI##########
1 | 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:
1 2 3 4 5 | 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"))
1 2 3 4 5 6 7 8 9 | 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)
1 2 3 | 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)
1 2 3 4 | 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)
1 2 3 4 5 6 7 8 | 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:
1 | 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:
1 2 3 | 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" )) |
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