gt gene set testing methods(globaltest)
gt gene set testing methods()所属R语言包：globaltest
Gene set testing of gene set databases using Global Test
基因组基因组数据库的测试，使用全球测试
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A collection of procedures for performing the Global Test on gene set databases. Three function are provided for KEGG, for Gene Ontology and for the Broad Institute's gene sets.
基因组数据库进行全球测试程序的集合。提供三个功能基因本体论为KEGG，为Broad研究所的基因套。
用法----------Usage----------
gtKEGG (response, exprs, ..., id, annotation, probe2entrez,
multtest = c("Holm", "BH", "BY"), sort = TRUE)
gtGO (response, exprs, ..., id, annotation, probe2entrez,
ontology = c("BP", "CC", "MF"), minsize=1, maxsize=Inf,
multtest = c("Holm", "focuslevel", "BH", "BY"),
focuslevel = 10, sort = TRUE)
gtConcept (response, exprs, ..., annotation, probe2entrez,
conceptmatrix, concept2name = "conceptID2name.txt",
entrez2concept = "entrezGeneToConceptID.txt", threshold = 1e-4,
share = TRUE, multtest = c("Holm", "BH", "BY"),
sort = TRUE)
gtBroad (response, exprs, ..., id, annotation, probe2entrez, collection,
category = c("c1", "c2", "c3", "c4", "c5"),
multtest = c("Holm", "BH", "BY"), sort = TRUE)
参数----------Arguments----------
参数：response
The response variable of the regression model. This is passed on to the response argument of gt.
回归模型响应变量。这是传递给responsegt参数。
参数：exprs
The expression measurements. May be ExpressionSet or matrix. Passed on to the alternative argument of gt.
表达测量。可能是ExpressionSet或矩阵。通过alternativegt论点。
参数：...
Any other arguments are also passed on to gt.
任何其他参数也传递到gt。
参数：id
The identifier(s) of gene sets to be tested (character vector). If omitted, tests all gene sets in the database.
基因识别码（S）设置进行测试（特征向量）。如果省略，测试数据库中的所有基因组。
参数：annotation
The name of the probe annotation package for the microarray that was used, or the name of the genome wide annotation package for the species (e.g. org.Hs.eg.db for human). If an organism package is given, the argument probe2entrez must be supplied. If annotation is missing, the function will attempt to retrieve the annotation information from the exprs argument.
探针使用的芯片，或物种基因组注释包（如人类org.Hs.eg.db）的名称标注包的名称。如果给出一个有机体包，参数probe2entrez必须提供。如果annotation丢失，该函数将尝试检索从exprs参数的注释信息。
参数：probe2entrez
Use only if no probe annotation package is available. A mapping from probe identifiers to entrez gene ids. May be an environment, named list or named vector.
只使用如果没有探针注解包是可用的。一个从探针标识符以Entrez基因IDS映射。可能是环境，命名列表或命名的向量。
参数：multtest
The method of multiple testing correction. Choose from: Benjamini and Hochberg FDR control (BH); Benjamini and Yekutieli FDR control (BY) or Holm familywise error fontrol (Holm). For gtGO also the focus level method is available. See focusLevel.
多次测试修正方法。选择：Benjamini和，HochbergFDR控制（BH）; Benjamini YekutieliFDR控制（）或霍尔姆族群误差fontrol（霍尔姆）。 gtGO还重点方法是可行的。看到focusLevel。
参数：sort
If TRUE, sorts the results to increasing p-values.
如果TRUE，各种增加p值的结果。
参数：ontology
The ontology or ontologies to be used. Default is to use all three ontologies.
要使用的本体或本体。默认是使用所有三个本体。
参数：minsize
The minimum number of probes that may be annotated to a gene set. Gene sets with fewer annotated probes are discarded.
注释基因组的探针可能的最小数目。注明探针较少的基因组将被丢弃。
参数：maxsize
The maximum number of probes that may be annotated to a gene set. Gene sets with more annotated probes are discarded.
注释基因组的探针，可能的最大数量。更多注明探针基因组将被丢弃。
参数：focuslevel
The focus level to be used for the focus level method. Either a vector of gene set ids, or a numerical level. In the latter case, findFocus is called with maxsize at the specified level to find a focus level.
重点一级用于重点级别的方法。无论是向量的基因组IDS，或数值水平。在后一种情况下，findFocus被称为maxsize在指定的水平，以找到一个焦点水平。
参数：collection
The Broad gene set collection, created by a call to getBroadSets.
广泛的基因组收集，调用getBroadSets由创建的。
参数：conceptmatrix
The name of the file containing the importance weights, i.e. concept profile associations between Anni concepts. In the matrix contained in the file, columns correspond to testable concepts, and rows correspond to entrez-concepts. Useable files can be downloaded from http://www.biosemantics.org/weightedglobaltest.
包含文件的重要性权重，即之间安妮概念概念的个人资料协会的名称。在该文件中包含的矩阵，列对应测试的概念，和行对应Entrez的概念。可以从http://www.biosemantics.org/weightedglobaltest下载可用的文件。
参数：concept2name
The name of the file containing a mapping between Anni concepts and entrez identifiers. Useable files can be downloaded from http://www.biosemantics.org/weightedglobaltest.
包含安妮的概念和Entrez标识符之间的映射文件的名称。可以从http://www.biosemantics.org/weightedglobaltest下载可用的文件。
参数：entrez2concept
The name of the file containing a mapping between Anni concept numbers and names. Useable files can be downloaded from http://www.biosemantics.org/weightedglobaltest.
的包含安妮概念号码和名称之间的映射文件的名称。可以从http://www.biosemantics.org/weightedglobaltest下载可用的文件。
参数：threshold
The relevance threshold for importance weights. Importance weights below the threshold are treated as zero.
重要性权重的相关性阈值。低于阈值的重要性权数视为零。
参数：share
If TRUE, the function divides the importance weight of a gene over all probes corresponding to the same entrez identifier. If FALSE, all probes get the full importance weight of the gene.
如果TRUE，功能划分，对应相同的Entrez的标识符对所有探针的一个基因的重要性重量。如果FALSE，所有探测器获得的基因完整的重要性重量。
参数：category
The subcategory of the Broad collection to be tested. The default is to test all sets.
广泛收集的子类别进行测试。默认是测试所有套。
Details
详情----------Details----------
These are utility functions to make it easier to do gene set testing of gene sets available in gene set databases. The functions automatically retrieve the gene sets, preprocess and select them, perform global test, do multiple testing correction, and sort the results on the basis of their p-values.
这些实用功能，使其更容易做基因组基因组，基因组数据库中测试。自动检索的功能基因组进行预处理，并选择他们，进行全球测试，做多个测试校正，p值的基础上进行排序的结果。
The four functions use different databases for testing. gtKEGG and gtGO use KEGG (http://www.genome.jp/kegg) and GO (http://www.geneontology.org); gtConcept uses the Anni database (http://www.biosemantics.org/anni), and gtBroad uses the MSigDB database (http://http://www.broadinstitute.org/gsea/msigdb). The gtConcept function differs from the other three in that it uses association weights between 0 and 1 for genes within sets, rather than having a hard cut-off for membership of a gene in a set.
四大功能使用不同的数据库进行测试。 gtKEGG和gtGO使用KEGG（http://www.genome.jp/kegg）的和GO（http://www.geneontology.org）;gtConcept使用安妮数据库（ http://www.biosemantics.org/anni），和gtBroad使用MSigDB数据库（http://http://www.broadinstitute.org/gsea/msigdb）的。 gtConcept函数不同于其他三个在集内的基因，它使用0和1之间的关联，而不是在一组基因的成员很难切断，重量。
All functions require that annotate and the appropriate annotation packages are installed. gtKEGG additionally requires the KEGG.db package; gtGO requires the GO.db package; gtBroad requires the user to download the XML file "msigdb_v2.5.xml" from \ http://www.broad.mit.edu/gsea/downloads.jsp, and to preprocess that file using the getBroadSets function. gtConcept requires files that can be downloaded from http://www.biosemantics.org/weightedglobaltest.
annotate和适当的注解包安装所有的功能要求。 gtKEGG另外需要KEGG.db包gtGO要求GO.db包gtBroad需要用户下载的XML文件“msigdb_v2.5.xml”从\http://www.broad.mit.edu/gsea/downloads.jsp，预处理，文件使用的getBroadSets功能。 gtConcept需要可以从http://www.biosemantics.org/weightedglobaltest下载的文件。
值----------Value----------
A gt.object.
Agt.object。
作者（S）----------Author(s)----------
Jelle Goeman: <a href="mailto:j.j.goeman@lumc.nl">j.j.goeman@lumc.nl</a>; Jan Oosting
参考文献----------References----------
参见----------See Also----------
The gt function. The gt.object and useful functions associated with that object.
gt函数。 gt.object和有用的与该对象相关的功能。
举例----------Examples----------
# Examples in the Vignette[例子中的小插曲]
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。
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发表于 2012-2-25 20:43:26
