ISAmiRNA(eisa)
ISAmiRNA()所属R语言包：eisa
Calculate (predicted) miRNA target enrichment for transcription
计算（预测）的miRNA转录目标富集
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function performs enrichment calculations with respect to predicted miRNA targets to check whether an ISA module contains many
这个函数执行富集miRNA的靶标方面的计算，以检查是否ISA模块包含许多
用法----------Usage----------
ISAmiRNA (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----------
miRNAs are short RNA fragments that specifically regulate (usually inhibit) the expression of genes. Some genes have been experimentally validated as targets of a given miRNA, but we currently don't know the target genes of most miRNAs.
miRNA是短的RNA片段，专门规范（通常抑制）基因的表达。一些基因已被实验验证为某一特定的miRNA的目标，但目前我们不知道的大多数miRNA的靶基因。
TargetScan is a database of predicted miRNA targets. The predictions are done based many factors, including the conservation of the target region during evolution.
TargetScan是一个数据库miRNA的靶标。预测做了许多因素，包括目标区域在进化过程中的保护。
The hypergeometric test, a version Fisher's exact test, takes a miRNA and a gene set (in our case coming from an ISA module) and asks whether the number of genes in the set regulated by the miRNA 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的miRNA和1的基因组（在我们的情况下从1的ISA模块）和询问的miRNA调控的一组基因的数量是否显著更多比什么（或更少）人会想到一个偶然的机会。
ISAmiRNA performs the hypergeometric test for every module, for all miRNAs in the TargetScan database.
ISAmiRNA执行miRNA的在TargetScan数据库的所有超几何测试，为每一个模块。
In order to use this function, TargetScan annotation packages are needed. These are currently available for Homo Sapiens and Mus Musculus and they can be downloaded from http://www.unil.ch/cbg/index.php?title=Software.
以使用此功能，需要TargetScan注解包。这些都是目前智人和小家鼠，他们可以从http://www.unil.ch/cbg/index.php?title=Software下载。
值----------Value----------
A miRNAListHyperGResult object.
一个miRNAListHyperGResult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----------
Thousands of Human Genes are MicroRNA Targets Benjamin P Lewis, Christopher B Burge, David P Bartel. Cell, 120:15-20 (2005).
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, ISAKEGG and ISACHR for other enrichment calculations.
ISAGO，ISAKEGG和ISACHR其他的富集计算。
The Category package.
Category包。
举例----------Examples----------
data(ALLModulesSmall)
if (require(targetscan.Hs.eg.db)) {
miRNA <- ISAmiRNA(ALLModulesSmall)
summary(miRNA, p=0.1)[[7]]
}
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 17:14:21
