R语言 Category包 HyperGResult-accessors()函数中文帮助文档(中英文对照)

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HyperGResult-accessors(Category)
HyperGResult-accessors()所属R语言包：Category

                                        Accessors for HyperGResult Objects
                                         为HyperGResult对象的存取

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This manual page documents generic functions for extracting data from the result object returned from a call to hyperGTest. The result object will be a subclass of HyperGResultBase. Methods apply to all result object classes unless otherwise noted.
本手册页的文件从调用hyperGTest从返回的结果对象中提取数据的通用功能。结果对象将是一个子类的HyperGResultBase。方法适用于所有结果对象类，除非另有说明。


用法----------Usage----------



pvalues(r)
oddsRatios(r)
expectedCounts(r)

geneCounts(r)
universeCounts(r)
universeMappedCount(r)
geneMappedCount(r)

geneIds(object, ...)
geneIdUniverse(r, cond = TRUE)
condGeneIdUniverse(r)
geneIdsByCategory(r, catids = NULL)
sigCategories(r, p)

## R CMD check doesn't like these
## annotation(r)
## description(r)

testName(r)
pvalueCutoff(r)
testDirection(r)

chrGraph(r)





参数----------Arguments----------

参数：r, object
An instance of a subclass of HyperGResultBase.
一个HyperGResultBase的子类的一个实例。


参数：catids
A character vector of category identifiers.
一类标识符的字符向量。


参数：p
Numeric p-value used as a cutoff for selecting a subset of the result.
数字p值作为选择的结果的一个子集的截止使用。


参数：cond
A logical value indicating whether to return conditional results for a conditional test.  The default is TRUE.  For non-conditional results, this argument is ignored.
一个逻辑值，指明是否返回的条件测试条件的结果。默认TRUE。对于非条件的结果，则忽略此参数。


参数：...
Additional arguments that may be used by specializing methods.
通过专业的方法，可使用额外的参数。


存取方法（通用功能）----------Accessor Methods (Generic Functions)----------




geneCounts returns an "integer" vector: for each category term tested, the number of genes from
geneCounts返回"integer"向量：每个类别的术语测试，基因




pvalues returns a "numeric"
pvalues返回"numeric"




universeCounts returns an "integer" vector: for each category term tested, the number of genes from
universeCounts返回"integer"向量：每个类别的术语测试，基因




universeMappedCount returns an "integer"
universeMappedCount返回"integer"




expectedCounts returns a "numeric" vector giving the expected number of genes in the selected gene list to be found at each tested category term.  These values may surprise you if you forget that your gene list and gene universe might have had to undergo further filtering to ensure that each gene has been
expectedCounts返回"numeric"向量给予的基因被发现在每个测试类别术语预期在选定的基因列表。这些值可能会让你大吃一惊，如果你忘了你的基因列表和基因宇宙可能不得不接受进一步的筛选，以确保每一个基因一直




oddsRatios returns a "numeric" vector giving
oddsRatios返回"numeric"向量给予




annotation returns the name
注释返回的名称




geneIds returns the input vector of gene identifiers intersected with the universe of
geneIds返回宇宙相交基因标识的输入向量




geneIdUniverse returns a list named by the tested categories.  Each element of the list is a vector of gene identifiers (from the gene universe) annotated at the
geneIdUniverse返回测试类别命名的名单。列表中的每个元素为向量的基因标识（从宇宙基因）在注释




geneIdsByCategory returns a list similar to geneIdUniverse, but each vector of gene IDs is intersected with the list of selected gene IDs from geneIds.  The result is the selected gene IDs annotated at
geneIdsByCategory返回一个列表类似geneIdUniverse，但每个基因标识的向量，是从geneIds相交选定的基因ID列表。结果是注明在选定的基因ID




sigCategories returns a character vector of category identifiers with a significant p-value.  If argument p is missing, then the cutoff obtained from pvalueCutoff(r) will
sigCategories返回一个显着的p值特征向量的类标识符。如果参数p丢失，然后从pvalueCutoff(r)将获得截止




geneMappedCount returns the size of the selected gene set used in the computation.  This is simply
geneMappedCount返回用于计算选定的基因组大小。这简直是




pvalueCutoff accessor for the
pvalueCutoff存取




testDirection accessor for the testDirection slot.  Contains a string indicating whether the test was for "over" or "under"
testDirection插槽testDirection存取。包含一个字符串，表示测试是否"over"或"under"




description returns a character
描述返回一个字符




testName returns a string
测试名返回一个字符串




isConditional returns TRUE if the
isConditional回报TRUE如果




summary returns a data.frame summarizing the test result.  Optional arguments pvalue and categorySize allow specification of maximum p-value and minimum categorySize,
摘要返回data.frame总结了测试结果。可选参数pvalue和categorySize允许的最大p值和最低categorySize规范，

The data frame contains the GOID, Pvalue, OddsRatio, ExpCount, Count, and Size.  ExpCount is the expected count and the Count is how many instances of that term were actually oberved in your gene list while the Size is the number that could have been found in your gene list if every instance had turned up.  Values like the ExpCount and the Size are going to be affected by what is included in the gene universe as well as by whether or not it was a conditional test.
数据框包含GOID，Pvalue，OddsRatio，ExpCount，Count，Size。 ExpCount是预期的计数和Count是多少，术语的实例，而实际上在你的基因列表obervedSize可能已经在你的基因列表的数量，如果每一个实例已经翻了起来。像值ExpCount和Size将要包括在基因宇宙以及与否，这是一个条件测试的影响。




htmlReport writes an HTML version of the table produced by the summary method.  The first argument should be a HyperGResult instance (or subclass). The path of a file to write the report to can be specified using the file argument.  The default is file="" which will cause the report to be printed to the screen.  If you wish to create a single report comprising multiple results you can set append=TRUE.  The default is FALSE (overwrite pre-existing report file).  You can specify a string to use as an identifier for each table by providing a value for the label argument.  The number of digits displayed in numerical columns can be controlled using digits (defaults to 3).  The summary method is called on the HyperGResult instance to generate a data frame that is transformed to HTML.  You can pass additional arguments to the summary method which is used to generate the data frame that is transformed to HTML by specifying a named
htmlReport写入summary方法产生的表的HTML版本。第一个参数应该是一个HyperGResult实例（或子类）。使用file参数，可以指定文件的路径写报告。默认的是file=""这会导致报告被打印到屏幕上。如果你想建立一个单一的报告，包括多个结果，你可以设置append=TRUE。默认是FALSE（覆盖现有的报告文件）。你可以指定一个字符串为每个表的标识符使用提供了价值label参数。使用digits（默认为3），可控制的数值列显示的位数。 summary方法被称为HyperGResult实例生成一个数据框转化为HTML。你可以传递额外的参数summary方法，它是用来生成数据框转化为HTML指定一个名为


作者（S）----------Author(s)----------


Seth Falcon



参见----------See Also----------

hyperGTest HyperGResult-class HyperGParams-class GOHyperGParams-class KEGGHyperGParams-class
hyperGTestHyperGResult-classHyperGParams-classGOHyperGParams-classKEGGHyperGParams-class


举例----------Examples----------


## Note that more in-depth examples can be found in the GOstats[＃注意，更深入的例子可以发现在GoStats上]
## vignette (Hypergeometric tests using GOstats).[＃小插曲（超几何测试使用GoStats上）。]
library("hgu95av2.db")
library("annotate")

probids <- ls(hgu95av2GENENAME)[1:300]
## Select for probeids that have PFAM ids[＃选择probeids PFAM IDS]
hasPFAM <- sapply(mget(probids, hgu95av2PFAM), function(ids)
                  if(!is.na(ids) &amp;&amp; length(ids) > 1) TRUE else FALSE)
probids <- probids[hasPFAM]
## get unique Entrez Gene IDs[＃获得独特的Entrez基因身份证]
probids <- unique(getLL(probids, "hgu95av2"))
## Now do the same for the universe[＃现在做宇宙]
univ <- ls(hgu95av2GENENAME)
univHasPFAM <- sapply(mget(univ, hgu95av2PFAM), function(ids)
                      if(!is.na(ids) &amp;&amp; length(ids) > 1) TRUE else
                         FALSE)
univ <- univ[univHasPFAM]
univ <- unique(getLL(univ, "hgu95av2"))

p <- new("PFAMHyperGParams", geneIds=probids, universeGeneIds=univ,
         annotation="hgu95av2")
## this takes a while...[＃这需要一段时间...]
if(interactive()){
hypt <- hyperGTest(p)
summary(hypt)
htmlReport(hypt, file="temp.html", summary.args=list("htmlLinks"=TRUE))
}

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


注：
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