KEGGREST包

linux从零开始

1、安装

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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
keggFind：Finds entries with matching query keywords or other query data in a given database
keggGet：Retrieves given database entries
keggInfo：Displays the current statistics of a given database
keggLink：Find related entries by using database cross-references.
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
3、每个对象的功能简单使用
3.1、keggConv（Convert KEGG identifiers to/from outside identifiers）
语法：keggConv(target, source, querySize = 100)
例子：
## conversion from NCBI GeneID to KEGG ID for E. coli genes##

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head(keggConv("eco", "ncbi-geneid"),2)
head(keggConv("ncbi-geneid", "eco"),2)
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）
语法：keggFind(database, query, option = c("formula", "exact_mass", "mol_weight"))
例子：

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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)
语法：keggGet(dbentries, option = c("aaseq", "ntseq", "mol", "kcf","image", "kgml"))
例子：

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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)
[/size][/font][font=comic sans ms, sans-serif][size=14px]keggGet("hsa05130", "kgml")

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3.4）keggInfo（Displays the current statistics of a given database）
语法:keggInfo(database)
例子：

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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.）
语法：keggLink(target, source)
例子：

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head(keggLink("pathway", "hsa")，5)
head(keggLink("hsa", "pathway")，5)
head(keggLink("pathway", c("hsa:10458", "ece:Z5100")),5)
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)
用法：keggList(database, organism)
例子：

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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.）
用法：listDatabases()
例子：

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listDatabases()
keggList("organism") ## list all organisms
keggList("hsa") ## list all human genes
keggList("genome") ## list all genome identifiers
keggList("T01001") ## list all human genes

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
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：

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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"))