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

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

                                         Output Tables Based on Hypergeometric Test
                                         投入产出表的基础上超几何测试

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This function will output various tables containing probesets that are annotated to a particular GO, KEGG, or PFAM term. The tables are based on the results from a call to hyperGtest.
此功能将输出包含probesets注明一个特定的GO，KEGG，或PFAM术语的各种表格。表是根据通话从到hyperGtest的结果。


用法----------Usage----------


hyperGoutput(hyptObj, eset, pvalue, categorySize, sigProbesets, fit = NULL,
subset = NULL,comp = 1, output = c("significant", "all", "split"),
statistics = c("tstat", "pval", "FC"), html = TRUE, text = TRUE, ...)



参数----------Arguments----------

参数：hyptObj
A HyperGResult object, usually produced by a call to hyperGTest  
一个HyperGResult对象，通常调用hyperGTest由生产


参数：eset
An ExpressionSet object
ExpressionSet对象


参数：pvalue
The p-value cutoff used for selecting significant GO terms. If not specified, it will be extracted from the HyperGResult object
用于选择显着的GO术语p值截止。如果没有指定，它将被HyperGResult对象提取


参数：categorySize
Number of terms in the universe required for a term to be significant. See details for more information
需要一个术语很大的宇宙数目。详情请参阅有关详细信息，


参数：sigProbesets
Vector of probeset IDs that were significant in the original analysis.  
向量，在原分析的的显著probeset ID。


参数：fit
An MArrayLM object, produced from a call to eBayes
MArrayLM对象，调用eBayes从生产


参数：subset
Numeric vector used to select particular tables to output. The default is to output tables for all terms. See details for more information
数字矢量用于选择特定的表输出。默认是输出表中的所有条款。详情请参阅有关详细信息，


参数：comp
Numeric vector of length one, used to indicate which comparison in the MArrayLM object to use for extracting relevant statistics. See details for more information
向量长度为1的数字，用于提取有关统计数字指示MArrayLM对象比较使用。详情请参阅有关详细信息，


参数：output
One of 'selected', 'all', or 'split'. See details for more information
一个选择，所有，或分裂。详情请参阅有关详细信息，


参数：statistics
Which statistics to output in the resulting tables. Choices include 'tstat', 'pval', or 'FC', corresponding to t-statistics, p-values, and fold change, respectively
统计数据中生成的表的输出。选择包括TSTAT，pval的“，或”界别“，对应的t-统计量，p值，和褶皱的变化，分别


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? Defaults to TRUE
布尔值。输出的文字表？ TRUE默认


参数：...
Allows end user to pass further arguments. The most notable would be an anncols argument, passed to probes2table to control the hyperlinked annotation columns. See aaf.handler for more information
允许最终用户通过进一步的论据。最引人注目的将是一个anncols参数，通过probes2table控制超链接注释列。看到aaf.handler更多信息


Details

详情----------Details----------

This function is designed to be used to output the results from a hypergeometric test for over-represented terms. This function would be used at the end of an analysis such as:
此功能被设计用来输出从超限额超几何测试的结果。此功能将被用于在分析，如：

1.) Compute expression values 2.) Fit a model using limma 3.) Output significant probesets using limma2annaffy 4.) Perform hypergeometric test using hyperGTest
1）计算表达式的值2）。使用limma3拟合模型。）输出显著probesets使用limma2annaffy4。）执行超几何测试使用hyperGTest

At step 4, one can output a list of the over-represented terms using htmlReport. One might then be interested in knowing which probesets contributed to the significance of a particular term, which is what this function is designed to do.
在第4步，就可以输出超限额使用htmlReport条款列表。然后，一个可能是兴趣知道这probesets特定字词的意义，这就是这个函数是专门做贡献。

One argument that can be passed to htmlReport (and also to hyperGoutput) is categorySize, which gives a lower bound for the number of probesets with a particular term in the universe. In other words, assume that a particular GO term is annotated to three probesets on a given chip. If, after doing a t-test to detect differentially expressed probesets, one of those probesets were found to be significantly differentially expressed and was then used to do a hypergeometric test, that GO term would be significant, with a small p-value. However, this is probably not very strong evidence that the GO term is actually over-represented, since there were only three to begin with. By setting categorySize to a sensible value (such as 10), this situation can be avoided.
一个参数，可以传递给htmlReport（也hyperGoutput）categorySize，它提供了一个较低的约束与宇宙中的一个特定术语的probesets。换句话说，假设一个特定的GO术语是注释probesets在一个给定的芯片。如果后做了t检验，检测，对这些probesets之一被发现显着差异表达，然后用来做超几何试验，去术语将显着，p值小，差异表达probesets的。然而，这可能是非常有力的证据的GO术语实际上是过度的代表，因为只有三个开始。通过设置categorySize到一个合理的值（如10），可避免这种情况。

This function will output HTML and/or text tables containing annotation information about each probeset as well as the expression values. In addition, if limma were used to fit the model, the relevant statistics (t-statistic, p-value, fold change) can also be output in the table by passing the MArrayLM object that resulted from a
此功能将输出HTML和/或文字表包含每个probeset以及表达式的值的注释信息。此外，如果limma被用来拟合模型，（t-统计量，p值，倍数变化）有关统计资料还可以输出通过MArrayLM对象的表中，从

call to eBayes. The statistics argument can
调用eBayes。 statistics参数

be used to control which statistics are output.
可以用来控制输出的统计。

By default hyperGoutput will output tables for all significant terms, which may end up being quite a few tables. Usually only a few terms are of interest, so there is a subset argument that can be used to select only those terms. This argument follows directly from the order of the table output by htmlReport or summary. For instance, if the first, third and fifth terms in the HTML table output by htmlReport were of interest, one would use subset=c(1,3,5).
由默认的hyperGoutput将输出表的所有重要条款，这可能最终被不少表。通常只有几方面的利益，所以是一个subset参数，可用于只选择那些条款。这种说法是直接从表输出htmlReport或summary秩序。例如，HTML表格输出第一，第三和第五方面htmlReport感兴趣的人会使用子集= C（1,3,5）。

One critical step prior to the hypergeometric test is to subset the probesets to unique Entrez Gene IDs. It should be noted however, that the functions used by hypergOutput will output all the probesets annotated to a particular term. The output argument is used to control this behavior. If output = "significant" (the default), then only those probesets that correspond to the original subsetting will be output. If output = "all", then all probesets will be output (grouped by Entrez ID), with the 'significant' probeset first. If output = "split", then all the probesets will be output, with all the 'significant' probesets first, followed by the other probesets, grouped by Entrez ID.
一个关键步骤前超几何测试子集probesets独特的Entrez基因标识。但应当指出，hypergOutput使用的功能将输出所有probesets注明一个特定的术语。 output参数是用来控制这种行为。如果输出=“显着”（默认），那么只有那些probesets对应的原子集将被输出。如果输出=“所有”，然后所有probesets将输出（Entrez的编号分组）显著“probeset的，第一。如果输出=“分裂”，那么所有probesets会输出，所有“重大”probesets其他Entrez的编号的分组probesets，，。

Note that the 'significant' probesets come from one of two sources. First, one can pass a character vector of probeset IDs corresponding to those that were significant in the original analysis (recommended). Second, if the geneIds slot of the GOHyperGParams object containes a named vector of Entrez Gene IDs, then the names from that vector will be used. This can be accomplished by using either findLargest or getUniqueLL.
需要注意的是“重大”probesets从两个来源之一。首先，可以通过了相应的probeset标识那些在原来的分析（推荐）显着的特征向量。第二，如果geneIds对象插槽GOHyperGParams中包含与Entrez基因ID的命名为向量，然后从该向量的名字将被用来。这可以通过使用任何findLargest或getUniqueLL。

Since the geneIds are by definition a unique set of Entrez Gene IDs, any duplicate probeset IDs will have been removed, so the first method is to be preferred for accuracy.
由于geneIds通过定义一套独特的Entrez基因标识，任何重复probeset ID的已被删除，所以第一种方法是要首选准确性。


值----------Value----------

This function returns no value, and is called solely for the side
这个函数没有返回值，纯粹为称为侧


作者（S）----------Author(s)----------


James W. MacDonald <jmacdon@med.umich.edu>



参见----------See Also----------

hyperGTest, htmlReport,
hyperGTest，htmlReport

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


注：
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