makeGOGraph(GOstats)
makeGOGraph()所属R语言包：GOstats
Construct a GO Graph
构建一个好图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The directed acyclic graph (DAG) based on finding the most specific terms for the supplied Entrez Gene IDs is constructed and returned. The constructuion is per GO ontology (there are three, MF, BP and CC) and once the most specific terms have been identified then all less specific terms are found (these are the parents of the terms) and then their parents and so on, until the root is encountered.
向无环图（DAG）在提供Entrez基因身份证寻找最具体的条款的基础上构造并返回。 constructuion是每的GO本体（主要有三种，MF，BP和CC）和一次最具体的条款已经确定，所有较具体的条款（这些条款的父母），然后他们的父母等，直到遇到根。
用法----------Usage----------
makeGOGraph(x, Ontology = "MF", removeRoot = TRUE, mapfun = NULL,
chip = NULL)
参数----------Arguments----------
参数：x
A vector of Entrez Gene IDs.
Entrez基因标识向量。
参数：Ontology
Which GO ontology to use (CC, BP, or MF).
哪去本体使用（CC，BP或MF）。
参数：removeRoot
A logical value indicating whether the GO root node should be removed or not.
一个逻辑值，指明是否应该被删除或不GO根节点。
参数：mapfun
A function taking a character vector of Entrez Gene IDs as its only argument and returning a list of "GO lists" matching the structure of the lists in the GO maps of annotation data packages. The function should behave similarly to mget(x, eg2gomap, ifnotfound=NA), that is, NA should be returned if a specified Entrez ID has no GO mapping. See details for the interaction of mapfun and chip.
一个函数的Entrez基因标识的特征向量作为其唯一的参数，并返回一个列表“GO列出匹配的GO注释数据包映射列表的结构。功能应该表现同样mget(x, eg2gomap, ifnotfound=NA)，就是NA应返回指定Entrez的ID有没有去映射。详情请参阅为mapfun和chip的互动。
参数：chip
The name of a DB-based annotation data package (the name will end in ".db"). This package will be used to generate an Entrez ID to GO ID mapping instead of mapfun.
一个DB-基于注解的数据包（名称将结束“。DB”）的名称。这个包将被用于产生Entrez的ID，ID映射，而不是去mapfun。
Details
详情----------Details----------
For each supplied Entrez Gene identifier all the GO annotations (in the specified ontology) are found. The mapping is achieved in one of three ways:
对于每一个提供的Entrez基因标识，所有好注解（在指定的本体）被发现。映射实现的三种方式之一：
If mapfun is provided, it will be used to perform the needed lookups. In this case, chip will be ignored.
如果mapfun提供，将用于执行所需的查找。在这种情况下，chip将被忽略。
If chip is provided and mapfun=NULL, then the needed lookups will be done based on the Entrez to GO mappings encapsulated in the specified annotation data package. This is the recommended usage.
如果chip是mapfun=NULL，然后将需要查找Entrez的去指定的注释数据包封装映射的基础上。这是推荐使用。
If mapfun and chip are NULL or missing, then the function will attempt to load the GO package (the environment-based package, distinct from GO.db). This package contains a legacy environment mapping Entrez IDs to GO IDs. If the GO package is not available, an error will be raised. Omitting both mapfun and chip is not recommended as it is not compatible with the DB-based annotation data packages.
如果mapfun和chip是NULL或丢失，那么该函数将尝试加载GO套件（基于环境的软件包，从GO.db不同）。这个软件包包含Entrez的一个遗留的环境映射的ID去标识。如果没有好包，一个错误将得到提升。省略双方mapfun和chip不建议，因为它是不兼容的DB-基于标注的数据包。
The mappings are different for the different ontologies. Typically a GO indentifier is used only in one specific ontology.
映射为不同的本体不同。典型的的GO indentifier是只在一个特定的本体。
The resulting structure is stored in a graph using the graph package, again from Bioconductor.
由此产生的结构存储在再次使用的Bioconductor，graph包，图。
值----------Value----------
An object that inherits from the graph class. The particular implementation is not specified.
对象graph类继承的。未指定特定的实现。
作者（S）----------Author(s)----------
R. Gentleman
参考文献----------References----------
<h3>See Also</h3>
举例----------Examples----------
library("hgu95av2.db")
set.seed(321)
uniqun <- function(x) unique(unlist(x))
gN <- uniqun(sample(hgu95av2ENTREZID, 4))
gg1 <- makeGOGraph(gN, "BP", chip="hgu95av2.db")
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 20:55:14
