ISAKEGG(eisa)
ISAKEGG()所属R语言包：eisa
Calculate KEGG Pathway enrichment for transcription modules
计算KEGG通路富集的转录模块
译者：生物统计家园网 机器人LoveR
描述----------Description----------
KEGG pathway enrichment is calculated for each ISA module separately. In the end the result is corrected for multiple hypothesis testing.
KEGG通路富集分别计算每个ISA模块。在最后的结果是纠正多个假设检验。
用法----------Usage----------
ISAKEGG (modules,ann = annotation(modules), features = featureNames(modules),
hgCutoff = 0.05, correction = TRUE, correction.method = "holm")
参数----------Arguments----------
参数：modules
An ISAModules object, a set of ISA modules.
ISAModules对象，一组的ISA模块。
参数：ann
Character scalar. The annotation package to be used. By default it is taken from the modules argument.
字符标。注释要使用的包。默认情况下它是取自modules参数。
参数：features
Character vector. The names of the features. By default it is taken from the modules argument.
特征向量。功能的名称。默认情况下它是取自modules参数。
参数：hgCutoff
Numeric scalar. The cutoff value to be used for the enrichment significance. This can be changed later, without recalculating the test.
数字标。截止值将用于充实意义。这是可以改变后，没有重新计算测试。
参数：correction
Logical scalar, whether to perform multiple hypothesis testing correction.
逻辑标量，是否执行多个假设检验校正。
参数：correction.method
Character scalar, the multiple testing correction method to use. Possible values: “holm”, “hochberg”, “hommel”, “bonferroni”, “BH”, “BY”, “fdr”, “none”. See the p.adjust function for details on these.
字符标量，使用多个测试校正方法。可能的值：“冬青”，“hochberg”，“HOMMEL”，“邦弗朗尼”，“波黑”，“”，“FDR”，“无”。见p.adjust这些细节功能。
Details
详情----------Details----------
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals. The PATHWAY database records networks of molecular interactions in the cells, and variants of them specific to particular organisms.
KEGG（京都基因和基因组百科全书）是一个在线数据库，收集与处理基因组，酶途径，生物化工。通路数据库记录在单元中的分子间的相互作用的网络，其中特别是生物体特定变种。
The hypergeometric test, a version Fisher's exact test, takes a KEGG pathway and a gene set (in our case coming from an ISA module) and asks whether the number of genes in the set participating in the pathway, is significantly more (or less) than what one would expect by chance.
的超几何试验，1版费舍尔的精确检验，需要1 KEGG通路和1的基因组（在我们的情况下从1的ISA模块），并询问是否该基因的参与途径的集数，是显著更多（或更少）比什么人会想到一个偶然的机会。
ISAKEGG performs the hypergeometric test for every module, for all KEGG pathways. The KEGG data is taken from the KEGG.db package and the annotation package of the chip.
ISAKEGG执行KEGG通路超几何试验，每个模块。 KEGG数据取自KEGG.db封装和芯片的注解包。
ISAKEGG currently cannot test for under-representation.
ISAKEGG目前无法测试的代表性不足。
值----------Value----------
A KEGGListHyperGResult object.
一个KEGGListHyperGResult对象。
作者（S）----------Author(s)----------
Gabor Csardi <a href="mailto:Gabor.Csardi@unil.ch">Gabor.Csardi@unil.ch</a>
参考文献----------References----------
resource for deciphering the genome, Nucleic Acids Res. 2004 Jan 1;32(Database issue) 277-80.
analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.
参见----------See Also----------
ISAGO, ISACHR, ISAmiRNA for other enrichment calculations.
ISAGO，ISACHR，ISAmiRNA其他的富集计算。
The KEGG.db and Category packages.
KEGG.db和Category包。
举例----------Examples----------
data(ALLModulesSmall)
KEGG <- ISAKEGG(ALLModulesSmall)
KEGG
sigCategories(KEGG)[[1]]
summary(KEGG)[[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 17:14:10
