getMipsInfo(ScISI)
getMipsInfo()所属R语言包：ScISI
A function that reads the downloaded text file from the MIPS
从MIPS读取下载的文本文件的函数
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function reads the downloaded text file from the MIPS database and parses the file for those collection of proteins either referred to as a "complex", an "-ase" (e.g. RNA Polymerase), or a "-some" (e.g. ribosome) and (or) user supplied terms as the protein complex of interest. It returns a list containing two items: a named list of protein complexes and a character vector (of the same length as the named list) describing each protein complex.
此功能从MIPS数据库下载的文本文件读取和解析那些收集蛋白质或者简称为“复杂”，“酶”（如RNA聚合酶）的文件，或“部分”（如核糖体）和（或）用户提供的蛋白质复合体的利益。它返回一个列表，其中包含两个项目：一个蛋白复合物和字符向量（命名为列表的长度相同），描述每个蛋白复合物的命名列表。
用法----------Usage----------
getMipsInfo(wantDefault = TRUE, toGrep = NULL,
parseType = NULL, eCode = c("901.01.03", "901.01.03.01", "901.01.03.02",
"901.01.04", "901.01.04.01", "901.01.04.02",
"901.01.05", "901.01.05.01", "901.01.05.02",
"902.01.09.02", "902.01.01.02.01.01",
"902.01.01.02.01.01.01", "902.01.01.02.01.01.02",
"902.01.01.02.01.02", "902.01.01.02.01.02.01",
"902.01.01.02.01.02.02", "902.01.01.04",
"902.01.01.04.01", "902.01.01.04.01.01",
"902.01.01.04.01.02", "902.01.01.04.01.03",
"902.01.01.04.02", "901.01.09.02"), wantSubComplexes=TRUE,
ht=FALSE, dubiousGenes=NULL)
参数----------Arguments----------
参数：wantDefault
A logical. If true, the default parameters "complex", "\Base\b" and "\Bsome\b" are grepped.
一个逻辑。如果为true，默认参数“复杂”，“\碱基\ B”和“\ Bsome \ B”grepped。
参数：toGrep
A character vector. Each entry is a term with perl regular expressions which are intended to be searched in the Mips text file.
字符向量。每个条目是一个术语用perl正则表达式是拟在MIPS的文本文件中搜索。
参数：parseType
A character vector. Each entry is a term that tells how each entry of toGrep should be parsed; e.g. "grep" or "agrep"
字符向量。每个条目是一个术语，告诉如何应解析每toGrep条目; “grep”的或“agrep”
参数：eCode
A character vector. The evidence code is given in the file evidence.scheme found in the inst/extdata section of the package.
字符向量。证据代码中发现INST / extdata节的包文件evidence.scheme。
参数：wantSubComplexes
A logical.If FALSE, the function only returns aggregate protein complexes. If TRUE, the function will also return subcomplexes as well.
一个logical.If FALSE，函数只返回总蛋白复合物。如果为TRUE，函数也将返回subcomplexes以及。
参数：ht
A logical. If FALSE, the function will not extract protein complex estimates obtained from high throughput analysis.
一个逻辑。如果为FALSE，函数将不能提取蛋白复合物高通量分析得到的估计。
参数：dubiousGenes
A character vector of genes that will be removed when parsing the MIPS repository.
特征向量的基因解析的MIPS库时将被删除。
Details
详情----------Details----------
This function's generic operation is to parse the Mips protein complex database (as given by the downloaded text file) and search for pre-determined or chosen terms. It returns a named list of chracter vectors where the names are MIPS id's from the protein complex sub-category and the vectors consist of proteins corresponding to that particular MIPS id. Running this function has multiple combinations:
此功能的通用操作是解析的MIPS蛋白质复合体的数据库（如下载的文本文件）和搜索预先确定或选择的条件。它返回了两性间的向量命名列表名称MIPS ID的蛋白复合物的子类和特定的MIPS ID对应的蛋白质组成的向量。运行这个函数有多种组合：
1. If the wantDefault parameter is TRUE, the function will grep for "complex", "\Base\b", and "\Bsome\b".
1。如果wantDefault参数为TRUE，函数将grep的“复杂”，“\碱基\ B”，“的\ Bsome \ B”。
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 MIPS 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拟在MIPS数据库搜索的条款和Perl的正则表达式。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 character vector consistin of MIPS evidence codes. A protein will be removed from the protein complex is ALL the evidence codes used to annotate the protein are supplied in the eCode argument; otherwise, it is left in the complex.
4。 eCode参数是的MIPS证据码字符向量consistin的。 A蛋白的蛋白复合物将拆除所有的证据用来注释的蛋白质在eCode参数提供的代码;否则，它是在复杂的离开。
5. If wantSubComplexes parameter is True, the function will return the sub-groupings (sub-complexes or sub-structures) as given by the clusterings in the MIPS protein complex database.
5。如果wantSubComplexes参数为True，该函数将返回MIPS蛋白质复杂的数据库聚类的子集团（子复合物或子结构）。
6. If ht parameter is True, the function will return the will return those protein complex estimates obtained from high throughput analysis as well.
6。如果HT参数为True，该函数将返回将返回估计从高通量分析，以及获得这些蛋白质复合体。
值----------Value----------
The return value is a list -
返回值是一个列表 -
参数：Mips
A named list of the protein complexes. Each list entry is denoted by some particlar MIPS ID (with the pre-fix "MIPS-") attachedand points to a character vector which are the members of that protein complex
命名的蛋白复合物的列表。每个列表项（前修复“的MIPS-”）attachedand点到一个字符向量，这是该蛋白复合物的成员由一些particlar MIPS的编号表示
参数：DESC
A named chracter vector describing each protein complex parsed by the function. (The names are the MIPS ID)
一个名为两性间的矢量描述每个蛋白质复合体的功能解析。 （名字是MIPS的ID）
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 13:55:32
