simLL(GOstats)
simLL()所属R语言包：GOstats
Functions to compute similarities between GO graphs and also
函数来计算之间的好图，也有相似之处
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Both simUI and simLP compute a similarity measure between two GO graphs. For simLL, first the induced GO graph for each of its arguments is found and then these are passed to one of simUI or simLP.
既simUI和simLP计算两个好图之间的相似性措施。为simLL，首先为它的每一个参数的诱导好图被发现，然后这些被传递到simUI或simLP。
用法----------Usage----------
simLL(ll1, ll2, Ontology = "MF", measure = "LP", dropCodes = NULL,
mapfun = NULL, chip = NULL)
simUI(g1, g2)
simLP(g1, g2)
参数----------Arguments----------
参数：ll1
A Entrez Gene ID as a character vector.
Entrez基因身份证作为一个特征向量的一个。
参数：ll2
A Entrez Gene ID as a character vector.
Entrez基因身份证作为一个特征向量的一个。
参数：Ontology
Which ontology to use ("MF", "BP", "CC").
本体使用（“MF”，“BP”，“消委会”）。
参数：measure
Which measure to use ("LP", "UI").
其中使用的措施（“LP”的“用户界面”）。
参数：dropCodes
A set of evidence codes to be ignored in constructing the induced GO graphs.
不容忽视的一组证据代码在构建诱导的GO图。
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。
参数：g1
An instance of the graph class.
graph类的一个实例。
参数：g2
An instance of the graph class.
graph类的一个实例。
Details
详情----------Details----------
For each of ll1 and ll2 the set of most specific GO terms within the ontology specified (Ontology) that are not based on any excluded evidence code (dropCodes) are found. The mapping is achieved in one of three ways:
每个ll1和ll2内指定的本体（Ontology）上没有任何排除证据代码的最具体的GO术语集（dropCodes）被发现的。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。
Next, the induced GO graphs are computed.
下一步，诱导的好图计算。
Finally these graphs are passed to one of simUI, (union intersection), or simLP (longest path). For simUI the distance is the size of the intersection of the node sets divided by the size of the union of the node sets. Large values indicate more similarity. These similarities are between 0 and 1.
最后，通过这些图表simUI（联盟路口），或simLP（最长路径）。 simUI距离节点路口设置由工会的节点集的大小划分的大小。大值，表明更多的相似性。这些相似之处是0和1之间。
For simLP the length of the longest path in the intersection graph of the two supplied graph. Again, large values indicate more similarity. Similarities are between 0 and the maximum leaf depth of the graph for the specified ontology.
simLP提供两个图形的交点图的最长路径的长度。再次，大值表示更多的相似性。相似之处是介于0和最大叶深度为指定的本体图。
值----------Value----------
A list with:
与名单：
参数：sim
The numeric similarity measure.
数字的相似性度量。
参数：measure
Which measure was used.
使用了哪些措施。
参数：g1
The graph induced by ll1.
ll1诱导的图形。
参数：g2
The graph induced by ll2.
ll2诱导的图形。
If one of the supplied Gene IDs does not have any GO terms associated with it, in the selected ontology and with the selected evidence codes then NA is returned.
如果所提供的基因ID不会有任何去与它相关的术语，在选定的本体与选定的证据代码，然后NA返回。
作者（S）----------Author(s)----------
R. Gentleman
参见----------See Also----------
makeGOGraph
makeGOGraph
举例----------Examples----------
library("hgu95av2.db")
eg1 = c("9184", "3547")
bb = simLL(eg1[1], eg1[2], "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 20:56:10
