KEGGpathway2reactionGraph(KEGGgraph)
KEGGpathway2reactionGraph()所属R语言包：KEGGgraph
Convert chemical reaction network of KEGG pathway into graph
转换成图KEGG通路的化学反应网络
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Regulatory pathways are always viewed as protein networks, so there is no 'reaction' information saved in their KGML files. Metabolic pathways are viewed both as both protein networks and chemical networks, hence the KEGGPathway-class object may have reactions information among chemical compounds.
总是被视为蛋白质网络监管途径，因此，有没有“反应”的信息保存他们KGML文件。代谢途径被视为蛋白质网络和化工网络，因此KEGGPathway-class对象可能有化合物之间的反应信息。
This functions extracts reaction information from KEGG pathway, and convert the chemical compound reaction network into directed graph.
这个功能提取KEGG通路反应信息，并转换成有向图的化合物反应网络。
用法----------Usage----------
KEGGpathway2reactionGraph(pathway, uniqueReaction = TRUE)
参数----------Arguments----------
参数：pathway
A KEGGPathway-class object, usually as the result of the function parseKGML
一个的KEGGPathway-class对象，通常作为结果的功能parseKGML
参数：uniqueReaction
logical, to indicate whether several chemical reactions (identified by different KEGG reaction ID) should be treated as one (TRUE) or many (FALSE)
逻辑，以指示是否应为（TRUE）或许多（FALSE），治疗几种化学反应（由不同KEGG反应ID标识）
Details
详情----------Details----------
The direction of the graph is specified by the role of the compound in the reaction, the edges goes always out of 'substrate' and points to 'product'.
图的方向是由指定的化合物反应的作用，边去总是“基材”和“产品”点。
For now there is no wrapper to parse the KGML file directly into a reaction graph. In future there maybe one, but we don't want to confuse users with two similar functions to parse the file into a graph (since we assume that most users will need the protein graph, which can be conveniently parsed by parseKGML2Graph).
现在有没有包装KGML文件直接解析成一个反应图。在未来有可能是一，但我们不希望用户混淆了两个类似的功能解析成一个图（该文件，因为我们认为大多数用户需要的蛋白质图，可以方便地解析parseKGML2Graph ）。
值----------Value----------
A directed graph with compounds as nodes and reactions as edges.
与边缘节点和反应的化合物图。
作者（S）----------Author(s)----------
Jitao David Zhang <a href="mailto:jitao_david.zhang@roche.com">mailto:jitao_david.zhang@roche.com</a>
参考文献----------References----------
<h3>See Also</h3>
举例----------Examples----------
mapfile <- system.file("extdata/map00260.xml",package="KEGGgraph")
map <- parseKGML(mapfile)
cg <- KEGGpathway2reactionGraph(map, uniqueReaction=FALSE)
cg
nodes(cg)[1:3]
edges(cg)[1:3]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 22:57:04
