gseaSignificance(phenoTest)
gseaSignificance()所属R语言包：phenoTest
ES' (enrichment scores) sifgnificance.
胚胎的（富集成绩）sifgnificance。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function performs the second step in the process of obtaining a GSEA-like plot. It computes the NES (normalized enrichment score), p values and fdr (false discovery rate) for all variables and signatures. A gseaSignaturesSign or gseaSignaturesVar object will be needed as input (these objects can be obtained with the gseaSignatures function). For an overview of the output use the summary method. The next step after using the gseaSignificance function would be using the plot method.
这个函数执行在获得GSEA般的图过程中的第二步。 NES的（归富集评分），p值和FDR（虚假的发现率）计算所有变量和签名。一个gseaSignaturesSign或gseaSignaturesVar对象将需要输入（这些对象可以得到gseaSignatures函数）。对于输出的概述，使用summary方法。 gseaSignificance函数将使用plot方法使用后的下一个步骤。
用法----------Usage----------
gseaSignificance(x,p.adjust.method='none',pval.comp.method='original',pval.smooth.tail=TRUE)
参数----------Arguments----------
参数：x
gseaSignaturesSign or gseaSignaturesVar object obtained with the gseaSignatures method. This object contains the enrichment scores ,the simulated enrichment scores and the fold changes or hazard ratios.
gseaSignaturesSign或gseaSignaturesVar对象gseaSignatures方法获得。此对象包含的丰富的分数，模拟富集分数和褶皱的变化或危险比。
参数：p.adjust.method
p adjustment method to be used. Common options are 'BH', 'BY', 'bonferroni' or 'none'. All available options and their explanations can be found on the p.adjust function manual.
P级调整的方法来使用。常用的选项是“波黑”，“由”，“邦弗朗尼或没有。 p.adjust函数手册上可以找到所有可用的选项和他们的解释。
参数：pval.comp.method
the p value computation method. Has to be one of 'signed' or 'original'. The default one is 'original'. See details for more information.
p值的计算方法。已经是一个“签名”或“原始”。默认的是“原始”。详情请参阅更多信息。
参数：pval.smooth.tail
if we want to estimate the tail of the ditribution where the pvalues will be generated.
如果我们想要估计的pvalues将会产生ditribution的尾。
Details
详情----------Details----------
The simulated enrichment scores and the calculated one are used to find the p value.
用来模拟富集分数计算p值。
P value calculation depends on the parameter pval.comp.method. The default value is 'original'. In 'original' we are simply computing the proportion of anbolute simulated ES which are larger than the observed absolute ES. In 'signed' we are computing the proportion of simulated ES which are larger than the observed ES (in case of having positive enrichment score) and the proportion of simulated ES which are smaller than the observed ES (in case of having negative enrichment score).
P值计算取决于参数pval.comp.method的。默认值是“原始”。在“原始”，我们只是计算的比例大于观测到的绝对ES anbolute模拟ES。在签署我们正在计算模拟的ES比例比观测到的ES（具有积极的富集得分的情况下）和模拟胚胎的比例都小于观测到的ES（在有负浓缩得分的情况下） 。
作者（S）----------Author(s)----------
Evarist Planet
参考文献----------References----------
Analysis. www.pnas.org/cgi/doi/10.1073/pnas.0506580102
in multiple testing. Computational Statistics & Data Analysis http://econpapers.repec.org/article/eeecsdana/v_3a51_3ay_3a2007_3ai_3a8_3ap_3a3885-3897.htm
举例----------Examples----------
#for examples see the help file of gseaSigntaures: ?gseaSignatures[看到的例子，gseaSigntaures帮助文件：gseaSignatures]
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 2012-2-26 11:05:13
