getGOInfo(ScISI)
getGOInfo()所属R语言包：ScISI
A function that parses through the GO database; it agreps for the term "complex" and greps suffixes "-ase" and "-some" and returns nodes
一个功能，通过GO数据库分析，它的术语“复杂”和greps后缀agreps“ASE”和“一些”，并返回节点
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function parses through the Cellular Component ontology for the GO nodes and searchs for the term "complex" or the suffix "-ase" (e.g. RNA Polymerase) or "-some" (e.g. ribosome) and (or) other user
此功能解析通过蜂窝组件本体的好节点和“复杂”或后缀“ASE”（如RNA聚合酶）或“一些”（如核糖体）和（或）其他用户searchs
用法----------Usage----------
getGOInfo(wantDefault = TRUE, toGrep = NULL,
parseType=NULL, eCode = NULL, wantAllComplexes = TRUE,
includedGOTerms=NULL, not2BeIncluded=NULL)
参数----------Arguments----------
参数：wantDefault
A logical. If TRUE, the default parameters ("complex", "\Base\b" and "\Bsome\b") are used.
一个逻辑。如果是TRUE，默认的参数（“复杂”，“\碱基\ B”和“\ Bsome \ B”）。
参数：toGrep
A character vector of the phrases (with Perl regular expressions) for which the function will parse through the GO database and search.
特征向量的短语（Perl正则表达式）通过GO数据库和搜索的功能解析。
参数：parseType
A character vector.This vector is in one to one correspondence with toGrep; it takes in the parse type such as "grep", "agrep", etc.
字符vector.This向量是一对一与toGrep的通信，需要在解析类型，如“grep”的“agrep”等
参数：eCode
A character vector of evidence codes (see "http://www.geneontology.org/GO.evidence.shtml" for details). The function will disallow any protein inclusion in the protein complexes if they are not indexed by evidence code other than those found in eCode.
一个证据编码字符向量（见“http://www.geneontology.org/GO.evidence.shtml”）。如果他们没有被索引比eCode发现的其他证据代码的功能将禁止任何在蛋白质复合物的蛋白质列入。
参数：wantAllComplexes
A logical. If TRUE, the function will incorporate all GO children of the nodes found by term searches. In addition, children of node GO:0043234 (the protein complex node) will also be incorporated.
一个逻辑。如果为TRUE，函数将纳入术语搜查发现的节点都去儿童。此外，节点的孩子：0043234（蛋白质复合体节点）也将被纳入。
参数：includedGOTerms
A character vector of GO terms that will be parsed regardless of the default and parseType parameters. In essence, these GO terms forced to be included.
一个将被解析，无论默认和parseType参数的GO术语的特征向量。从本质上讲，这些GO术语被迫被列入。
参数：not2BeIncluded
A character vector of GO terms that should not be parsed nor included in the output.
GO术语不应该被解析，也不包含在输出中的一个特征向量。
Details
详情----------Details----------
This function's generic operation is to parse the GO database and search for pre-determined or chosen terms. It returns a named list of chracter vectors where the names are GO id's from the CC ontoloy and the vectors consist of proteins corresponding to that particular GO id. Running this function has multiple combinations:
此功能的通用操作解析GO数据库和搜索预先确定或选择条款。它返回一个命名的名字是好ID的消委会ontoloy和向量，特别是好ID对应的蛋白质组成的两性间的向量列表。运行这个函数有多种组合：
1. If the wantDefault parameter is TRUE, the function will agrep for "complex" and grep for "\Base\b" and "\Bsome\b".
1。 ，如果wantDefault参数是TRUE，函数将agrep“复杂”和“\碱基\ B”和“的\ Bsome \ B”的grep。
2. If toGrep is not NULL, it will be a character vector with terms and perl regular expressions that are intended for searching in the GO database. NB - it toGrep is not NULL, then parseType should also not be NULL as the parseType indicates how each term should be searched.
2。如果toGrep不为NULL，这将是一个特征向量的条款和Perl的正则表达式搜索GO数据库的。注意 - 它toGrep不为NULL，然后parseType应该也不会是NULL parseType表示每学期应如何搜索。
3. parseType needs to be supplied if toGrep is not NULL. It is a character vector, either a single entry or of length equal to the length of toGrep, detailing how each term in toGrep will be parsed in the GO database. If only one term is supplied for parseType, then all the terms in toGrep will be parsed identically. Otherwise, the i-th term in parseType will reflect the parsing of the i-th term in toGrep.
3。 parseType需要提供如果toGrep不为NULL。这是一个特征向量，无论是单次入境或长度等于的toGrep的长度，详细介绍了如何在toGrep每个任期将在GO数据库分析。如果只有一个术语提供parseType，然后所有在toGrep条款将被解析相同。否则，parseType在第i个任期将反映i个术语在toGrep解析。
4. The eCode argument is a user determined refining mechanism. It takes in a vector of evidence codes (as detailed by the GO website). The function will dis-allow proteins if and only if these proteins are only indexed by evidence codes found within eCodes.
4。的eCode说法是炼机制确定用户。需要（详见由GO网站）在证据代码的向量。该函数将显示允许蛋白质当且仅当这些蛋白质仅由内eCodes发现的证据码索引。
5. If wantAllComplexes parameter is True, the function will also return the children of nodes found by parsing terms. In addition, the children of GO ID GD:0043234 (the protein complex ID) will be returned. The union of complexes is then returned.
5。如果wantAllComplexes参数为True，功能也将返回解析方面发现的节点的孩子。此外，孩子：好编号粤0043234（蛋白质复合体的ID）将被退回。复合物的结合，然后返回。
值----------Value----------
The return value is a list of size n (n depends on the current status of the GO database) where the name of each list element is a GO ID and each list element itself is a character vector consisting of the proteins corresponding to a particular GO ID:
返回值是一个大小为n（N GO数据库的当前状态而定），其中每个列表元素的名称是一个好身份证，每个列表元素本身是一个字符对应一个特定的GO的蛋白质组成的向量列表编号：
参数："GO:XXXXXXX"
A character vector containing proteins (not indexed by only eCode evidence codes) which make up protein complex "GO:XXXXXXXX"
含有蛋白质的一个特征向量（只eCode证据代码索引）蛋白复合物的“GO：XXXXXXXX的”
作者（S）----------Author(s)----------
Tony Chiang
参考文献----------References----------
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 2012-2-26 13:55:18
