R语言 affycoretools包 vennSelect()函数中文帮助文档(中英文对照)

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vennSelect(affycoretools)
vennSelect()所属R语言包：affycoretools

                                        Select and Output Genelists Based on Venn Diagrams
                                         选择和基于维恩图输出Genelists上

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This function is designed to output text and/or HTML tables based on the results of a call to decideTests.
此功能设计到输出的文本和/或HTML表的基础上的调用decideTests一个结果。


用法----------Usage----------


vennSelect(eset, design, x, contrast, fit, method = "same", adj.meth =
"BH", stat = "fstat", otherstats = c("pval","FC"), order.by = "pval",
foldFilt = NULL, save = 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：...
Used to pass other arguments to probes2table, in particular, to change the argument to anncols  which controls the columns of hyperlinks to online databases (e.g., Entrez Gene, etc.). See aaf.handler for more information.
用来传递其他参数probes2table，特别是，要改变的参数anncols控制线上资料库（例如，Entrez基因等）的超链接列。看到aaf.handler更多信息。


Details

详情----------Details----------

The purpose of this function is to output HTML and text tables with lists of genes that fulfill the criteria of a call to decideTests as well as the direction of differential expression.
此功能的目的是为了输出HTML和文字表实现调用decideTests以及差异表达的方向一个标准的基因名单。

Some important things to note: First, the names of the HTML and text 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，HTML和文本表的名字的colnames对象，这从对比矩阵TestResults中提取的，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 and text tables:
调用函数通常会导致在输出HTML和文字表：

vennSelect(eset, fit, design, x)
vennSelect（ESET，装配，设计，X）

Calling the function with save set to TRUE will output both HTML and text 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将输出HTML和文字表以及每个比较计数向量的功能。这是有用的，当使用函数编程（例如，当使用Sweave的决策报告）。

out <- vennSelect(eset, fit, design, x, save = TRUE)
出< -  vennSelect（ESET，装配，设计，X，保存= 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 and text 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和文本表的副作用。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 &lt;jmacdon@med.umich.edu&gt;

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
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