ISAGO(eisa)
ISAGO()所属R语言包：eisa
Calculate Gene Ontology enrichment for transcription modules
计算基因的转录模块本体富集
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Gene Ontology enrichment is calculated for each ISA module separately. In the end the result is corrected for multiple hypothesis testing.
基因本体富集计算分别为每个ISA模块。在最后的结果是纠正多个假设检验。
用法----------Usage----------
ISAGO (modules, ann = annotation(modules), features = featureNames(modules),
hgCutoff = 0.05, correction = TRUE, correction.method = "holm")
参数----------Arguments----------
参数：modules
An ISAModules object, a set of ISA modules.
ISAModules对象，一组的ISA模块。
参数：ann
Character scalar. The annotation package to be used. By default it is taken from the modules argument.
字符标。注释要使用的包。默认情况下它是取自modules参数。
参数：features
Character vector. The names of the features. By default it is taken from the modules argument.
特征向量。功能的名称。默认情况下它是取自modules参数。
参数：hgCutoff
Numeric scalar. The cutoff value to be used for the enrichment significance. This can be changed later, without recalculating the test.
数字标。截止值将用于充实意义。这是可以改变后，没有重新计算测试。
参数：correction
Logical scalar, whether to perform multiple hypothesis testing correction.
逻辑标量，是否执行多个假设检验校正。
参数：correction.method
Character scalar, the multiple testing correction method to use. Possible values: “holm”, “hochberg”, “hommel”, “bonferroni”, “BH”, “BY”, “fdr”, “none”. See the p.adjust function for details on these.
字符标量，使用多个测试校正方法。可能的值：“冬青”，“hochberg”，“HOMMEL”，“邦弗朗尼”，“波黑”，“”，“FDR”，“无”。见p.adjust这些细节功能。
Details
详情----------Details----------
The Gene Ontology is a database of gene annotation. The annotating labels (these are called terms) are standardized and organized into a directed acyclic graph. In other words terms may have more specific sub-terms, that can have even more specific sub-sub-terms, and so on.
基因本体论是一个数据库的基因注释。标准化组织成一个有向无环图的注释标签（这是所谓的条款）。换句话说，可能有更具体的子项，可以有更具体的分包条款，等等。
The Gene Ontology database has three big sub-graphs, the root nodes (the most general terms) of these are the direct children of the root term of the whole ontology: biological process, cellular component, molecular function. They are usually referred to as ontologies.
基因本体数据库有三个大的子图，根节点（最通用的条款）这些都是整个本体的根术语的直接子：生物过程，单元成分，分子功能。他们通常简称为本体。
The hypergeometric test, a version Fisher's exact test, takes a GO term and a gene set (in our case coming from an ISA module) and asks whether the number of genes in the set annotated by the term is significantly more (or less) than what one would expect by chance.
在超几何试验，1版本费舍尔的精确检验，需要1好术语和1的基因组（在我们的情况下从1的ISA模块）和询问的一套术语注释的基因数是否显著更多（或更少）比什么人会想到一个偶然的机会。
ISAGO performs the hypergeometric test for every module, for all GO terms of the three GO ontologies. The GO data is taken from the GO.db package and the annotation package of the chip.
ISAGO执行每个模块的超几何试验，所有三个基因本体GO术语。 GO数据取自GO.db封装和芯片的注解包。
ISAGO currently cannot test for under-representation and the conditional test, as implemented in the GOstats package, is not available either.
ISAGO目前还不能代表和GOstats包实施的条件测试，测试，是不是可以。
值----------Value----------
A list with three GOListHyperGResult objects, for the three Gene Ontologies, named
与3GOListHyperGResult对象名单，三个基因本体命名，
参数：BP
aka Biological Processes
又名生物过程
参数：CC
aka Cellular Components
又名单元成分
参数：MF
aka Molecular Function
又名分子作用
作者（S）----------Author(s)----------
Gabor Csardi <a href="mailto:Gabor.Csardi@unil.ch">Gabor.Csardi@unil.ch</a>
参考文献----------References----------
of biology. Nat. Genet. May 2000;25(1):25-9.
analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.
参见----------See Also----------
ISAKEGG, ISACHR, ISAmiRNA for other enrichment calculations.
ISAKEGG，ISACHR，ISAmiRNA其他的富集计算。
The GO.db, GOstats and Category packages.
GO.db，GOstats和Category包。
举例----------Examples----------
data(ALLModulesSmall)
GO <- ISAGO(ALLModulesSmall)
GO
summary(GO$BP)[[1]][,1:5]
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 17:13:49
