makeGeneRepresentation(Genominator)
makeGeneRepresentation()所属R语言包：Genominator
Compute a gene representation from annotation.
计算从注释的基因表示。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Computing a gene representation from annotation using a variety of methods.
注释从使用各种方法计算的基因表示。
用法----------Usage----------
makeGeneRepresentation(annoData, type = c("UIgene", "Ugene", "ROCE",
"background"), gene.id = "ensembl_gene_id", transcript.id = "ensembl_transcript_id", bind.columns, ignoreStrand = TRUE, verbose = getOption("verbose"))
参数----------Arguments----------
参数：annoData
A data frame which must contain the columns chr, start, end and strand which specifies annotation regions of interest, and optionally additional columns.
一个数据框，其中必须包含列chr，start，end和strand指定注释区域的利益，和可选的附加列。
参数：type
The type of gene representation, see details.
基因表现的类型，看到的细节。
参数：gene.id
The column in annoData that holds the gene identifiers (only needed for certain types of representation).
在annoData列拥有的基因标识（只需要某些类型的代表）。
参数：transcript.id
The column in annoData that holds the transcript identifiers (only needed for certain types of representation).
在annoData列持有的成绩单标识符（只需要某些类型的代表）。
参数：bind.columns
A character vector of column names that will be kept in the return object. It is assumed (but not checked) that these values are constant for all regions in a gene.
列名称将保持在返回对象的一个特征向量。据推测（但不检查）这些值是固定在一个基因的所有区域。
参数：ignoreStrand
Is strand ignored? Little testing has been done for the value 'TRUE'.
被忽略链？小测试已经完成，为“TRUE”的价值。
参数：verbose
Want verbose output?
想要详细的输出吗？
Details
详情----------Details----------
A union representation (Ugene) is simply the union of all bases of all transcripts of the gene, with bases belonging to other genes removed.
仅仅是一个工会代表（Ugene）联盟的所有基因转录的所有碱基，碱基属于其他基因删除。
A union-intersection representation (UIgene) for a gene is defined as bases that are annotated as belonging to all transcripts of the gene, and not to any other gene.
一个路口工会代表基因（UIgene）被定义为碱基，是属于所有转录的基因，而不是任何其他基因的注解。
Regions of constant expression (ROCE) are regions where one would assume that the expression is constant. They are best explained by an example: if transcript A goes from 1 to 4 and transcript B goes from 1 to 6 there are two ROCEs, one from 1 to 4 and one from 5 to 6. It is possible to define ROCEs independent of the gene concept, but in its current implementation regions belonging to more than one gene are removed.
常量表达式（资本收益率）的区域是其中一个假设，表达的是不变的区域。他们是最好的解释了一个例子：如果成绩单一个从1到4和成绩单乙从1到6，有两个ROCEs，从1到4和1 5日至6。它是可能的基因概念的定义ROCEs独立，但在其目前实施的区域属于一个以上的基因被删除。
Background is essentially the complement of the annotation.
背景基本上是注释的补充。
值----------Value----------
A data.frame with rownames and columns chr, strand, start, end, and possibly additional columns.
一个data.frameCHR，钢绞线，开始，结束，可能还有其他列rownames和列。
作者（S）----------Author(s)----------
James Bullard <a href="mailto:bullard@berkeley.edu">bullard@berkeley.edu</a>, Kasper Daniel Hansen
<a href="mailto:khansen@jhsph.edu">khansen@jhsph.edu</a>
举例----------Examples----------
data(yeastAnno)
ui <- makeGeneRepresentation(yeastAnno, type = "background")
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 19:32:04
