vennSelectBM(affycoretools)
vennSelectBM()所属R语言包：affycoretools
Select and Output Genelists Based on Venn Diagrams using biomaRt
选择和维恩图使用biomaRt基于输出Genelists上
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function is designed to output HTML and text tables based on the results of a call to decideTests. This function is very similar to vennSelect, except it uses the biomaRt package to annotate genes, and the annotate package to create the HTML table.
此功能被设计来输出HTML和文本的基础上的调用decideTests一个结果表。此功能是非常相似的vennSelect，除非它使用biomaRt包注释基因，annotate包创建HTML表。
用法----------Usage----------
vennSelectBM(eset, design, x, contrast, fit, method = "same", adj.meth = "BH",
stat = "fstat", otherstats = c("pval", "FC"), order.by = "pval",
foldFilt = NULL, save = FALSE, species, links = linksBM()[1:3],
otherdata = annBM()[1:3], ann.source = "entrezgene",
html = TRUE, text = TRUE, affyid = FALSE, ...)
参数----------Arguments----------
参数：eset
A ExpressionSet object.
一个ExpressionSet对象。
参数：design
A design matrix, usually from a call to model.matrix. See details for more information.
一个design矩阵，通常由调用model.matrix。详情请参阅更多信息。
参数：x
A TestResults object, usually from a call to decideTests.
一个TestResults对象，通常从decideTests的呼叫。
参数：contrast
A contrasts matrix, produced either by hand, or by a call to makeContrasts
一个对比矩阵，手工制作，或由一个makeContrasts呼叫
参数：fit
An MArrayLM object, from a call to eBayes.
MArrayLM对象，从eBayes调用。
参数：method
One of "same", "both", "up", "down", "sameup", or "samedown". See details for more information.
一个“不变”，“既”，“向上”，“打倒”，“sameup”，或“samedown”。详情请参阅更多信息。
参数：adj.meth
Method to use for adjusting p-values. Default is 'BH', which corresponds to 'fdr'. Ideally one would set this value to be the same as was used for decideTests.
调整p值的方法来使用。默认值是“波黑”，“FDR”对应。理想的情况下，将设置这个值是相同的是decideTests。
参数：stat
The statistic to report in the resulting HTML tables. Choices are 'fstat', 'tstat', and NULL. Ideally, the statistic chosen would correspond to the method used in decideTests. In other words, if one used methods such as 'separate' or 'hierarchical', which are based on a t-statistic, one should choose 'tstat', however, if one used 'nestedF', the logical choice would be 'fstat'.
统计报告中所产生的HTML表格。选择是FSTAT，TSTAT，NULL。理想的情况下，所选择的统计对应decideTests使用的方法，。换句话说，如果一个使用方法，如独立或层次，这是基础上的t-统计，应选择“TSTAT”，但是，如果使用“nestedF”，逻辑选择将是FSTAT “。
参数：otherstats
Other statistics to be included in the HTML tables. Choices include 'pval' and 'FC'.
其他被列入统计的HTML表。选择包括pval的“和”财委会“。
参数：order.by
Which statistic should be used to order the probesets? Choices include 'fstat', 'tstat', 'pval', and 'FC'. Note that if 'FC' is chosen and there are more than one set of fold changes, the first will be used.
统计数据应责令probesets？选择包括FSTAT，TSTAT，pval的“，”功能界别“。请注意，如果FC的选择，有超过一组倍的变化，首先将使用。
参数：foldFilt
A fold change to use for filtering. Default is NULL, meaning no filtering will be done.
用于过滤的fold change。默认的NULL，这意味着没有过滤将。
参数：save
Boolean - If TRUE, output a count of genes that fulfill the criteria. Useful for e.g., Sweave-type reports.
Boolean - 如果TRUE，输出符合标准的基因计数。例如有用，Sweave型报告。
参数：species
The species name. This must be in a particular format for biomaRt. An example for human is "hsapiens", or for mouse "mmusculus".
物种的名称。这必须是在一个特定的格式为biomaRt。为人类的例子是的“hsapiens”或“鼠标”mmusculus的。
参数：links
A character vector of things to annotate with hyperlinks to online databases. See linksBM for possible values.
一个事物的特征向量与网上数据库的超链接注释。看到linksBM可能的值。
参数：otherdata
A character vector of things to annotate with text only (i.e., no hyperlinks). See annBM for possible values.
的东西，只用文字注释的特征向量（即，没有超链接）。看到annBM可能的值。
参数：ann.source
The annotation source of the IDs that will be used to annotate the genes. The default value is "entrezgene". See details for other possibilities.
的，将被用来注释基因标识标注来源。默认值是“entrezgene”。详情请参阅其他的可能性。
参数：html
Boolean. Output HTML tables? Defaults to TRUE
布尔值。输出HTML表格？ TRUE默认
参数：text
Boolean. Output text tables? Defaulst to TRUE
布尔值。输出的文字表？ defaulst到TRUE
参数：affyid
Boolean. Are the IDs used to annotate these data Affymetrix IDs?
布尔值。用来注释这些数据Affymetrix公司标识的ID吗？
参数：...
Used to pass other variables to e.g., htmlpage.
用于通过其他变量，例如，htmlpage。
Details
详情----------Details----------
The purpose of this function is to output HTML tables with lists of genes that fulfill the criteria of a call to decideTests as well as the direction of differential expression.
此功能的目的是输出HTML表格与实现调用decideTests以及差异表达的方向一个标准的基因名单。
The IDs that will be used to annotate the genes depend on the source of the data. If, for example, one is using an Affymetrix chip that doesn't have a BioC annotation package, then the IDs will be Affymetrix IDs. To find out the correct name to use for the ann.source argument, one can create a connection to a Biomart database using useMart and then deduce the correct argument by the output from listFilters(mart). It will usually be something starting with 'affy', and contain the name of the chip.
将用来注释基因的ID取决于数据源。例如，如果使用Affymetrix公司的芯片，没有BioC的注解包，然后ID将是Affymetrix公司的ID。找出正确的名称，使用为ann.source参数，可以使用useMart然后推断正确的参数，从listFilters(mart)输出到Biomart数据库创建一个连接。它通常会是affy开始，包含芯片的名称。
If one is using one of the re-mapped CDFs from MBNI at University of Michigan, then the IDs to use depend on the mapping used to create the CDF. At this time, only three types of CDFs can be used; EntrezGene, UniGene, and RefSeq. One can determine the correct ann.source argument by creating a connection to a Biomart database, and then calling linksBM(mart, linksBM())[[3]].
如果一个人在密歇根大学从MBNI使用重新映射CDFS之一，然后标识使用取决于用于创建的CDF映射。在这个时候，只有三个类型CDFS可以使用; EntrezGene，UniGene的，和的RefSeq。一个由创建一个到Biomart数据库的连接，可以判断正确ann.source参数，然后调用linksBM(mart, linksBM())[[3]]。
Some important things to note: First, the names of the HTML tables are extracted from the colnames of the TestResults object, which come from the contrasts matrix, so it is important to use something descriptive. Second, the method argument is analogous to the include argument from vennCounts or vennDiagram. Choosing "both" will select genes that are differentially expressed in one or more comparisons, regardless of direction. Choosing "up" or "down" will select genes that are only differentially expressed in one direction. Choosing "same" will select genes that are differentially expressed in the same direction. Choosing "sameup" or "samedown" will select genes that are differentially expressed in the same direction as well as 'up' or 'down'.
一些重要的事情要注意：首先，提取HTML表格的名称colnamesTestResults对象，这从对比矩阵，所以重要的是要使用的东西描述。二，方法的参数是类似于include或vennCounts参数vennDiagram。选择“双方”将选择是在一个或多个比较差异表达的基因，无论方向。选择“向上”或“下降”的选择，只在一个方向的差异表达的基因。选择“同”会选择在同一个方向的差异表达基因。选择“sameup”或“samedown”将选择在同一方向，以及“向上”或“下”差异表达的基因。
Note that this is different than sequentially choosing "up" and then "down". For instance, a gene that is upregulated in one comparison and downregulated in another comparison will be listed in the intersection of those two comparisons if "both" is chosen, it will be listed in only one comparison for both the "up" and "down" methods, and it will be listed in the union (e.g., not selected) if "same" is chosen.
请注意这是不同于依次选择“向上”，然后“关闭”。例如，在一个比较上调和下调另一个比较基因将在十字路口，如果“双方”选择这两个比较上市，将上市只在一个比较，无论是“向上”和“向下”的方法，将列出联盟（例如，未选中），如果选择了“相同的”。
Calling the function normally will result in the output of HTML tables.
调用函数通常会导致在输出HTML表格。
Calling the function with save set to TRUE will output HTML tables as well as a vector of counts for each comparison. This is useful when using the function programmatically (e.g., when making reports using Sweave).
调用保存设置TRUE的功能将输出HTML表格以及每个比较计数向量。这是有用的，当使用函数编程（例如，当使用Sweave的决策报告）。
out <- vennSelectBM(eset, fit, design, x, <other arguments>, save = TRUE)
出< - vennSelectBM（ESET，装配，设计，X，<其他arguments>的储存= TRUE）
An alternative would be to use vennCounts2 and vennDiagram to output a Venn diagram, which is probably more reasonable since the tables being output are supposed to be based on a Venn diagram.
另一种方法是使用vennCounts2和vennDiagram输出，这可能是比较合理的，因为输出的表都被认为是基于维恩图维恩图。
值----------Value----------
Normally called only for the side effect of producing HTML tables. However, setting save to TRUE will output a vector of counts that can be used for making Sweave-style reports.
通常被称为只产生HTML表格的副作用。但是，设置保存到TRUE将输出一个Sweave风格的报告，可以使用数的向量。
作者（S）----------Author(s)----------
James W. MacDonald <jmacdon@med.umich.edu>
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 11:14:21
