ListHyperGResult-class(eisa)
ListHyperGResult-class()所属R语言包：eisa
Classes for quick GO/KEGG/CHR/miRNA target or other enrichment
为快速，GO / KEGG /人权/ miRNA靶或其他浓缩的类
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These classes extend the HyperGResult class from the Category package to perform enrichment calculation quickly for multiple gene sets.
这些类扩展HyperGResult类Category包快速进行多个基因组富集计算。
用法----------Usage----------
## S4 method for signature 'ListHyperGResult'
summary(object, pvalue = pvalueCutoff(object),
categorySize = NULL)
## S4 method for signature 'ListHyperGResult'
htmlReport(r, file = "", append = FALSE,
label = "", digits = 3, summary.args = NULL)
## S4 method for signature 'ListHyperGResult'
pvalues(r)
## S4 method for signature 'ListHyperGResult'
sigCategories(r, p)
## S4 method for signature 'ListHyperGResult'
geneCounts(r)
## S4 method for signature 'ListHyperGResult'
expectedCounts(r)
## S4 method for signature 'ListHyperGResult'
oddsRatios(r)
## S4 method for signature 'ListHyperGResult'
universeCounts(r)
## S4 method for signature 'ListHyperGResult'
geneMappedCount(r)
## S4 method for signature 'ListHyperGResult'
universeMappedCount(r)
## S4 method for signature 'ListHyperGResult'
geneIdsByCategory(r, catids = NULL)
## S4 method for signature 'ListHyperGResult'
geneIdUniverse(r, cond = FALSE)
参数----------Arguments----------
参数：object,r
A ListHyperGResult object.
一个ListHyperGResult对象。
参数：pvalue,p
Numeric vector of length one, the p-value limit, up to which the terms are listed.
数字矢量长度，p值的限制，到哪个条款列出。
参数：categorySize
A numeric vector of length one, or NULL. If not NULL, then it gives the minimum number of annotated genes in the universe, in order to list the term.
数字矢量的长度，或NULL。如果没有NULL，然后它使宇宙中的注释基因的最低数量，以列出的术语。
参数：file
A file name, or a connection object. The result is written here. If it is "", then the result is written to the standard output. If it is NULL, then the result is not written anywhere. (But it is always returned, invisibly, see below.)
一个文件名，或者一个连接对象。结果写在这里。如果是的话""，然后结果被写入到标准输出。如果是NULL，那么结果是没有写在任何地方。 （但无形的，它总是返回，见下文。）
参数：append
Logical scalar, whether to append the HTML code to the given file, or remove its previous contents if it already exists.
逻辑标量，是否追加给定的文件的HTML代码，或删除其以前的内容，如果它已经存在。
参数：label
An HTML label (<A LABEL=""> tag) to add.
添加的HTML标签（<A LABEL="">标签）。
参数：digits
The number of digits to use for the numeric columns.
数字列使用的位数。
参数：summary.args
A list of arguments to pass to the summary method.
列表中的参数传递给summary方法。
参数：catids
The categories for which the genes are listed. All categories will be listed if this argument is NULL.
基因的类别列出。如果这种说法是NULL，将列出所有类别。
参数：cond
Currently not used.
目前没有使用。
Details
详情----------Details----------
A ListHyperGResult object can store the results of hypergeometric tests, several gene sets against the same universe. ListHyperGRresult is an extension of HyperGResult, as defined in the Category package.
一个ListHyperGResult对象可以存储超几何测试的结果，几个基因对同一宇宙中设置。 ListHyperGRresult是扩展HyperGResult，在Category包的定义。
More precisely, ListHyperGResult is an abstract class, it is not possible to instantiate objects from it. Its extensions are be used instead: GOListHyperGResult, KEGGListHyperGResult, CHRListHyperGResult and miRNAListHyperGResult.
更确切地说，ListHyperGResult是一个抽象类，它是不可能实例化的对象。其扩展用来代替：GOListHyperGResult，KEGGListHyperGResult，CHRListHyperGResult和miRNAListHyperGResult。
值----------Value----------
pvalues, geneCounts, expectedCounts, oddsRatios and universeCounts return a list of named numeric vectors.
pvalues，geneCounts，expectedCounts，oddsRatios和universeCounts返回一个列表命名的数字向量。
geneMappedCount returns a numeric vector, universeMappedCount returns a numeric vector of length one.
geneMappedCount返回一个数值向量，universeMappedCount返回一个长度为1的数字向量。
sigCategories returns a list of character vectors.
sigCategories返回一个字符向量列表。
geneIdsByCategory returns a list of lists of character vectors.
geneIdsByCategory返回一个字符向量名单列表。
geneIdUniverse returns a list of character vectors.
geneIdUniverse返回一个字符向量列表。
summary returns a list of data frames with columns: "Pvalue", "OddsRatio", "ExpCount", "Count", "Size" and optionally "drive".
summary返回的列的数据框列表：“Pvalue，OddsRatio，ExpCount”，“伯爵”，“大小”，可选“驱动器”。
htmlReport returns a list of chracter vectors, invisibly.
htmlReport返回一个列表两性间的向量，无形之中。
conditional returns a logical vector of length one. ontology returns a character vector of length one.
conditional返回一个长度为1的逻辑向量。 ontology返回一个长度为1的特征向量。
成员函数----------Member functions----------
Most of the member functions are analogous to the ones defined for HyperGResult in the Category package. Usually the only difference is that they return a list of vectors, with one entry for each gene set, instead of just a single vector.
大多数成员函数的类似于HyperGResultCategory包中定义的。通常情况下，唯一的区别是他们返回向量的列表，每个基因组中的一个条目，而不仅仅是一个单一的向量。
pvalues returns the p-values of the hypergeomatric tests. A list is returned, with one numeric vector entry for each input gene set. The p-values for each gene set are ordered according to decreasing significance.
pvalues返回p-的hypergeomatric测试值。返回一个列表，每个输入基因组的一个数值向量入口。 p每个基因组的值是有序的根据递减意义。
geneCounts returns the number of genes from the gene set that are annotated with the given term. This is returned for all input gene sets, in a list.
geneCounts返回从基因组的基因是与给定的术语注明数量。这将返回所有输入基因组，在列表中。
expectedCounts returns the number of genes that are expected to be annotated with the given term, just by chance. This is calculated for all input gene sets, and returned as a list.
expectedCounts返回注明是用给定的期限，只是偶然的机会，预期的基因数目。这是计算所有输入基因组，并作为一个列表返回。
oddsRatios returns the odds ratios for each term tested, for all gene sets, in a list of numeric vectors.
oddsRatios返回胜算比为每学期进行测试，所有基因组中一个数值向量列表。
universeCounts returns the number of genes from the universe that are annotated with the given term, for all gene sets, in a list.
universeCounts返回从宇宙基因是与给定的术语注明数量，所有的基因组，在一个列表。
geneMappedCount gives the size of the gene sets, as used in the algorithm. This can be different than the size of the input gene sets, because of the elimination of duplicates and genes that are not in the universe, before the actual computation.
geneMappedCount给基因组的大小，所使用的算法。这可能是输入基因组的大小不同，因为消除重复和基因是在宇宙中不前，实际计算。
universeMappedCount gives the size of the gene universe, as used in the computation. This can be different than the size given by the user, because duplicates are eliminated before the computation.
universeMappedCount给基因宇宙的大小，在计算使用。这可能是由用户给定的大小不同，因为重复计算之前消除。
sigCategories returns the significant terms, at the given p-value threshold, for all gene sets, as a list.
sigCategories返回的重要条款，在给定的p值阈值，所有基因组，作为一个列表。
geneIdsByCategory returns a list of lists, one entry for each input gene set. Every entry is a list itself and for each tested term it gives the gene ids from the gene set that are annotated with the given term.
geneIdsByCategory返回一个列表，为每个输入基因组中的一个条目。每个条目本身是一个列表，每个测试来看，它使从基因的基因组与给定的术语注明IDS。
geneIdUniverse returns a list of character vectors, one for each term that was tested, giving the ids of the genes from the universe that are annotated with that term.
geneIdUniverse返回特征向量，每个被测试的术语，从宇宙中，这个词注释基因的ID。
summary returns a list of data frames, one for each input gene set. Each data frame has columns: "Pvalue", "OddsRatio", "ExpCount", "Count", "Size" and optionally "drive". Each row of the data frame corresponds to a tested term.
summary返回一个数据框，一个为每个输入基因组的列表。每个数据框列：Pvalue，OddsRatio，ExpCount“，”伯爵“，”大小“和”驱动器“（可选）。每行对应的数据框的测试项。
htmlReport creates a HTML summary from a ListHyperGParams object. This consists of one table for each input gene get. The summary can be written to a file, but it is also returned in a list of character vectors. There is one list entry for each input gene set, and each element of the character vector corresponds to one line of HTML code. You need the xtable package to use this function.
htmlReport从ListHyperGParams对象创建一个HTML摘要。这包括为每个输入基因得到一个表。摘要可以被写入到一个文件，但它也返回特征向量。为每个输入基因组有一个列表项，每个元素对应的特征向量一行HTML代码。你需要xtable包使用此功能。
The following functions are defined for GOListHyperGResult objects only.
GOListHyperGResult对象只被定义为以下功能。
conditional returns a logical vector of length one, whether the test was conditional or not. Conditional testing is currently not implemented, please see the GOstats package for a working implementation.
conditional返回一个长度为1的逻辑向量，测试是否是有条件的或不。目前尚未实施条件测试，请GOstats包看到一个工作的实施。
ontology returns a character vector of length one, the name of the ontology for the GO test.
ontology返回特征向量的长度为一，本体的GO测试的名称。
作者（S）----------Author(s)----------
Gabor Csardi <a href="mailto:Gabor.Csardi@gmail.com">Gabor.Csardi@gmail.com</a>
参见----------See Also----------
Functions for enrichment calculation of ISA modules: ISAGO, ISAKEGG, ISACHR, ISAmiRNA, ISAEnrichment.
ISA的富集计算功能模块：ISAGO，ISAKEGG，ISACHR，ISAmiRNA，ISAEnrichment。
Perhaps see also the vignette in the GOstats package.
或许也看到GOstats包中的小插曲。
举例----------Examples----------
data(ALLModulesSmall)
GO <- ISAGO(ALLModulesSmall)
GO$CC
sigCategories(GO$CC)[[1]]
summary(GO$CC)[[1]][,1:5]
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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 17:15:11
