R语言 siggenes包 EBAM-class()函数中文帮助文档(中英文对照)

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EBAM-class(siggenes)
EBAM-class()所属R语言包：siggenes

                                        Class EBAM
                                         类EBAM

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This is a class representation for the Empirical Bayes Analysis of Microarrays (EBAM) proposed by Efron et al. (2001).
这是一个类的经验Bayes分析埃弗龙等人提出的微阵列（EBAM）表示。 （2001年）。


类的对象----------Objects from the Class----------

Objects can be created using the function ebam.
创建对象可以使用的功能ebam。


插槽----------Slots----------




z: Object of class "numeric" representing the
z：Object类的"numeric"代表




posterior: Object of class "numeric" representing
posterior：Object类的"numeric"代表




p0: Object of class "numeric" specifying the
p0：Object类的"numeric"指定




local: Object of class "numeric" consisting of the
local：Object类的"numeric"组成




mat.fdr: Object of class "matrix" containing general statistics such as the number of differentially expressed genes and
mat.fdr：Object类的"matrix"含有差异表达基因的数量，如一般的统计数字，




a0: Object of class "numeric" specifying the used value of the fudge factor. If not computed, a0 will be
a0：Object类的"numeric"指定的值蒙混因素。如果不计算，a0会




mat.samp: Object of class "matrix" containing the permuted group labels used in the estimation of the null distribution. Each row represents one permutation, each column one observation (pair). If no permutation procedure has been used,
mat.samp：Object类的"matrix"含有置换组在空分布的估计使用的标签。每一行代表一个排列，每列一个观察（对）。如果没有置换的程序已被使用，




vec.pos: Object of class "numeric" consisting of the number of positive permuted test scores that are absolutely larger than the test score of a particular gene for each gene.
vec.pos：Object类的"numeric"积极置换的考试成绩是绝对的每一个基因的一个特定基因的测试得分比数组成。




vec.neg: Object of class "numeric" consisting of the number of negative permuted test scores that are absolutely larger than the test score of a particular gene for each gene.
vec.neg：Object类的"numeric"负置换的考试成绩是绝对的每一个基因的一个特定基因的测试得分比数组成。




msg: Object of class "character" containing information about, e.g., the type of analysis. msg is printed when the functions
msg类"character"包含的信息，例如，类型的分析对象。 msg打印功能时




chip: Object of class "character" naming the microarray used in the analysis. If no information about the chip is available,
chip：Object类的"character"命名在分析中使用的芯片。如果没有提供有关芯片的信息是，


方法----------Methods----------




plot signature(object = "EBAM"): Generates a plot of the posterior probabilities of the genes for a specified value of  Delta. For details, see help.ebam(plot). For
图signature(object = "EBAM")：生成一个基因的后验概率为指定的值Delta图。有关详细信息，请参阅help.ebam(plot)。为




print signature(object = "EBAM"): Prints general information such as the number of differentially expressed genes and the estimated FDR for several values of Delta. For details, see
打印signature(object = "EBAM")：打印的差异表达基因的数量和Delta几个值估计FDR，如一般的信息。有关详情，请参阅




show signature(object = "EBAM"): Shows the output of an
显示signature(object = "EBAM")：显示输出




summary signature(object = "EBAM"): Summarizes the results of an EBAM analysis for a specified value of Delta. For details, see help.ebam(summary). For the arguments,
总结signature(object = "EBAM")：总结为指定的值Delta一个EBAM分析结果。有关详细信息，请参阅help.ebam(summary)。为参数，


作者（S）----------Author(s)----------


Holger Schwender, <a href="mailto:holger.schw@gmx.de">holger.schw@gmx.de</a>



参考文献----------References----------

of a Microarray Experiment, JASA, 96, 1151-1160.
the Empirical Bayes and the Significance Analysis of Microarrays. Technical Report, SFB 475, University of Dortmund, Germany.

参见----------See Also----------

ebam, find.a0, FindA0-class
ebam，find.a0，FindA0-class


举例----------Examples----------


  # Load the data of Golub et al. (1999) contained in the package multtest.[Golub等装入的数据。 （1999年）载包multtest。]
  data(golub)
  
  # golub.cl contains the class labels.[golub.cl包含类的标签。]
  golub.cl
  
  # Perform an EBAM analysis for the two class unpaired case assuming[两个类未成的假设情况下执行EBAM分析]
  # unequal variances. Specify the fudge factor a0 by the suggested[异方差。建议指定软糖因子A0]
  # choice of find.a0[可选择的find.a0]
  find.out <- find.a0(golub, golub.cl, rand = 123)
  ebam.out <- ebam(find.out)
  ebam.out
   
  # Obtain the number of differentially[获得的差异]
  # expressed genes and the FDR if a gene is called differentially[基因表达和FDR，如果一个基因的差异被称为]
  # expressed if its posterior probability is larger than 0.8, 0.85,[表示，如果它的后验概率大于0.8，0.85，]
  # 0.9, 0.95.[0.9，0.95。]
  print(ebam.out, c(0.8, 0.85, 0.9, 0.95))
   
  # Generate a plot of the posterior probabilities for delta = 0.9.[生成后验概率为δ= 0.9的图。]
  plot(ebam.out, 0.9)
   
  # Obtain the list of genes called differentially expressed if their[获得列表称为差异表达的基因，如果他们]
  # posterior probability is larger than 0.99, and gene-specific [后验概率大于0.99，特定基因]
  # statistics for these variables such as their z-value and their[这些变量，如z值及其统计]
  # local FDR.[当地FDR。]
  summary(ebam.out, 0.9)
  


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


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