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

loveR · 发表于 2012-2-26 07:37:40

EBMTP-class(multtest)
EBMTP-class()所属R语言包：multtest

 Class "EBMTP", classes and methods for empirical Bayes multiple testing procedure output
 EBMTP“类”，类和方法经验Bayes多个测试程序输出

 译者：生物统计家园网机器人LoveR

描述----------Description----------

An object of class EBMTP is the output of a particular multiple testing procedure, as generated by the function EBMTP. The object has slots for the various data used to make multiple testing decisions, in particular adjusted p-values.
类EBMTP的对象是一个特定的多个测试程序的输出，功能EBMTP。对象插槽使用的各种数据，使多个测试决定，调整，特别是P-值。

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

Objects can be created by calls of the form new('MTP', statistic = ...., object of class numeric estimate = ...., object of class numeric sampsize = ...., object of class numeric rawp = ...., object of class numeric adjp = ...., object of class numeric reject = ...., object of class matrix rawdist = ...., object of class matrix nulldist = ...., object of class matrix nulldist.type = ...., object of class character marg.null = ...., object of class character marg.par = ...., object of class matrix label = ...., object of class numeric falsepos = ...., object of class matrix truepos = ...., object of class matrix errormat = ...., object of class matrix EB.h0M = ...., object of class numeric prior = ...., object of class numeric prior.type= ...., object of class character lqv = ...., object of class numeric Hsets = ...., object of class matrix index = ...., object of class matrix call = ...., object of class call seed = ...., object of class integer )
对象可以创建新的参考（“中期计划”，参考统计的形式调用= ...，对象类数字参考估计= ......，对象类数字参考sampsize = ...，对象类数字参考rawp = ......，对象类数字参考adjp = ......，类数字参考对象拒绝= ......，对象类矩阵参考rawdist = ......，对象类矩阵参考nulldist = ......，对象类矩阵参考nulldist.type = ......，阶级性的对象参考玛格NULL = ....，阶级性参考marg.par对象......，类矩阵参考标签的对象......，对象类的数字参考falsepos = ... ，对象类矩阵参考truepos = ......，对象类矩阵参考errormat = ......，对象类矩阵参考EB.h0M = ......，类对象数字参考之前......，对象类的数字参考prior.type = ......，阶级性参考lqv对象= ...，数字参考Hsets类对象。 ...，对象类矩阵参考指数= ......，对象类矩阵参考呼叫= ......，对象的类调用参考种子= ......，对象类的整数参考）

插槽----------Slots----------

statistic Object of class numeric, observed test statistics for each hypothesis, specified by the values of the MTP arguments test, robust, standardize, and psi0.
statisticObject类的numeric，每一种假说，观察测试统计的MTP参数的值指定test，robust，standardize ，psi0。

estimate For the test of single-parameter null hypotheses using t-statistics (i.e., not the F-tests), the numeric vector of estimated parameters corresponding to each hypothesis, e.g. means, differences in means, regression parameters.
estimate例如：对于单参数的空假设，参数估计的数字矢量对应每一种假说，t-统计量（即F检验）测试方法，手段的差异，回归参数。

sampsize Object of class numeric, number of columns (i.e. observations) in the input data set.
sampsizeObject类的numeric，在输入数据集的列数（即观察）。

rawp Object of class numeric, unadjusted, marginal p-values for each hypothesis.
rawp类numeric，未经调整，边际每个假设P-值的对象。

adjp Object of class numeric, adjusted (for multiple testing) p-values for each hypothesis (computed only if the get.adjp argument is TRUE).
adjp类numeric，调整（多个测试），每一种假说P-值（仅计算get.adjp参数为TRUE）的对象。

reject Object of class 'matrix', rejection indicators (TRUE for a rejected null hypothesis), for each value of the nominal Type I error rate alpha.
rejectObject类的'matrix'，抑制指标（拒绝零假设为真），每个标称值类型错误率alpha。

rawdist The numeric matrix for the estimated nonparametric non-null test statistics distribution (returned only if keep.rawdist=TRUE and if nulldist is one of 'boot.ctr', 'boot.cs', or 'boot.qt'). This slot must not be empty if one wishes to call update to change choice of bootstrap-based null distribution.
rawdist只有keep.rawdist=TRUE如果nulldist是一个“boot.ctr，boot.cs”，或估计非参数非空试验的统计分布的数值矩阵（返回boot.qt）。这个插槽不能是空的，如果人们想打检测update改变引导为主的空分布的选择。

nulldist The numeric matrix for the estimated test statistics null distribution (returned only if keep.nulldist=TRUE). By default (i.e., for nulldist='boot.cs'), the entries of nulldist are the null value shifted and scaled bootstrap test statistics, with one null test statistic value for each hypothesis (rows) and bootstrap iteration (columns).
nulldist估计检验统计量的零分布的数字矩阵（如果keep.nulldist=TRUE返回）。默认情况下（即nulldist='boot.cs'），参赛nulldist转移和缩放的引导测试统计每个假设一个空测试统计值（行）和引导迭代（列）的空值，。

nulldist.type Character value describing which choice of null distribution was used to generate the MTP results. Takes on one of the values of the original nulldist argument in the call to MTP, i.e., 'boot.cs', 'boot.ctr', 'boot.qt', or 'ic'.
nulldist.type字符值描述空分布的选择是用来产生中期计划的结果。注意到原nulldist在中期计划，即“boot.cs，boot.ctr”，“boot.qt，或IC调用的参数值之一。

marg.null If nulldist='boot.qt', a character value returning which choice of marginal null distribution was used by the MTP. Can be used to check default values or to ensure manual settings were correctly applied.
marg.null如果nulldist='boot.qt'，中期计划用边际空分布的选择是由一个字符值返回。可用于检查默认值，以确保手动设置正确适用。

marg.par If nulldist='boot.qt', a numeric matrix returning the parameters of the marginal null distribution(s) used by the MTP. Can be used to check default values or to ensure manual settings were correctly applied.
marg.par如果nulldist='boot.qt'，中期计划（S）的边际空分布的参数返回一个数字矩阵。可用于检查默认值，以确保手动设置正确适用。

falsepos A matrix with rows equal to the number of hypotheses and columns the number of samples of null test statistics (B) indicating the number of guessed false positives when using the corresponding value of the observed test statistic as a cut-off. Not returned unless keep.falsepos=TRUE.
falsepos一个假设和列空测试统计的样本数（B）指示数等于矩阵的行猜到误报时，使用相应的观测试验统计值截断。除非keep.falsepos=TRUE没有回来。

truepos A matrix with rows equal to the number of hypotheses and columns the number of samples of null test statistics (B) indicating the number of guessed true positives when using the corresponding value of the observed test statistic as a cut-off. Not returned unless keep.truepos=TRUE.
truepos一个指示空测试统计的样本数（B）猜测真阳性时，使用相应的观测试验统计值的假设和列数等于矩阵的行截断。除非keep.truepos=TRUE没有回来。

errormat The matrix obtained after applying to type I error rate function closure to the matrices in falsepos, and, if applicable, truepos. Not returned unless keep.errormat=TRUE.
errormat申请键入falsepos我的错误率函数的闭包矩阵，如果适用，“truepos后得到的矩阵。除非keep.errormat=TRUE没有回来。

EB.h0M The sum of the local q-values obtained after density estimation. This number serves as an estimate of the proportion of true null hypotheses. Values close to one indicate situations in which type I error control may not be guaranteed by the EBMTP. When prior='EBLQV', this value is used as the prior 'pi' during evaluation of the local q-value function.
EB.h0M密度估计后得到当地的Q值的总和。作为一个真正的零假设的比例估计这个数字。值接近1表明，在I型误差控制，不得由EBMTP保证的情况下。当prior='EBLQV'，这个值被用来作为前“PI”在当地的Q-值函数的评价。

prior The numeric value of the prior 'pi' used when evaluating the local q-value function.
prior之前的“圆周率”的数值，评估当地的Q-值函数时使用。

prior.type Character string returning the value of prior in the original call to EBMTP. One of 'conservative', 'ABH', or 'EBLQV'.
prior.type字符串返回值priorEBMTP原来的呼叫。一个“保守”，“陆地棉”，或“EBLQV”。

lqv A numeric vector of length the number of hypotheses with the estimated local q-values used for generating guessed sets of true null hypotheses.
lqv一个数值向量长度的假设与估计Q值用于产生真正的零假设猜测套。

Hsets A numeric matrix with the same dimension as nulldist, containing the Bernoulli realizations of the estimated local q-values stored in lqv which were used to partition the hypotheses into guessed sets of true and false null hypotheses at each round of (re)sampling. Not returned unless keep.Hsets=TRUE.
Hsets一个nulldist，含有伯努利变卖估计本地lqv猜到真正集被用来假设分区中存储的Q值和相同尺寸的数字矩阵在每一轮（重）抽样虚假的零假设。除非keep.Hsets=TRUE没有回来。

label If keep.label=TRUE, a vector storing the values used in the argument Y. Storing this object is particularly important when one wishes to update EBMTP objects with F-statistics using default marg.null and marg.par settings when nulldist='boot.qt'.
label如果keep.label=TRUE，存储参数Y值矢量。存储这个对象就显得尤为重要，当一个人希望更新F-统计使用默认的marg.null和marg.par设置nulldist='boot.qt'EBMTP对象。

index For tests of correlation parameters a matrix corresponding to t(combn(p,2)), where p is the number of variables in X. This matrix gives the indices of the variables considered in each pairwise correlation. For all other tests, this slot is empty, as the indices are in the same order as the rows of X.
index相关参数测试矩阵对应t(combn(p,2))，其中p是变量X的数量。这个矩阵给出了考虑的变量在每个成对相关的指标。对于所有其他的测试，这个槽是空的，指数在作为X的行的顺序相同。

call Object of class call, the call to the MTP function.
callObject类的call，中期计划功能的调用。

seed An integer or vector for specifying the state of the random number generator used to create the resampled datasets. The seed can be reused for reproducibility in a repeat call to MTP. This argument is currently used only for the bootstrap null distribution (i.e., for nulldist="boot.xx"). See ?set.seed for details.
seed整数或指定用于创建重采样的数据集随机数发生器的状态向量。种子可重复使用的重复性在重复调用MTP。这种说法目前只能用于引导空分布（即nulldist="boot.xx"）。看到?set.seed详情。

方法----------Methods----------

signature(x = "EBMTP") 
signature(x = "EBMTP")参考

[ : Subsetting method for EBMTP class, which operates selectively on each slot of an EBMTP instance to retain only the data related to the specified hypotheses.
[：EBMTP类，经营选择性EBMTP实例的每个插槽只保留到指定的假说有关的数据子集的方法。

as.list : Converts an object of class EBMTP to an object of class list, with an entry for each slot.
as.list：转换为对象类的一个对象类EBMTPlist，每个插槽的条目。

plot : plot methods for EBMTP class, produces the following graphical summaries of the results of a EBMTP. The type of display may be specified via the which argument. 
图：图EBMTP类，方法产生的一个EBMTP的结果下面的图形摘要。通过which参数，显示类型可以指定。参考

1. Scatterplot of number of rejected hypotheses vs. nominal Type I error rate. 
1。散点图的名义I型错误率与拒绝的假设。参考

2. Plot of ordered adjusted p-values; can be viewed as a plot of Type I error rate vs. number of rejected hypotheses. 
2。图的有序调整p值，可以作为一个类型的图，我的错误率与拒绝假说。参考

3. Scatterplot of adjusted p-values vs. test statistics (also known as "volcano plot"). 
3。散点图，调整后的P-值与测试统计数据（也称为“火山图”）。参考

4. Plot of unordered adjusted p-values. 
4。图的无序调整的p值。参考

The plot method for objects of class EBMTP does not return the plots associated with which=5 (using confidence regions) or with which=6 (pertaining to cut-offs) as it does for objects of class MTP. This is because the function EBMTP currently only returns adjusted p-values. The argument logscale (by default equal to FALSE) allows one to use the negative decimal logarithms of the adjusted p-values in the second, third, and fourth graphical displays. The arguments caption and sub.caption allow one to change the titles and subtitles for each of the plots (default subtitle is the MTP function call). Note that some of these plots are implemented in the older function mt.plot.
EBMTP类的对象的图方法不which=5（置信区间）或which=6（关于削减权衡）返回类对象，因为它的图MTP。这是因为函数EBMTP目前只返回p-值调整。参数logscale（默认等于FALSE）允许使用负的十进制调整后的P-值的对数，在第二，第三和第四的图形显示。参数caption和sub.caption“允许一个改变每个图（默认字幕是MTP函数调用）的标题和字幕。请注意，这些图的一些旧的功能mt.plot实施。

print : print method for EBMTP class, returns a description of an object of class EBMTP, including sample size, number of tested hypotheses, type of test performed (value of argument test), Type I error rate (value of argument typeone), nominal level of the test (value of argument alpha), name of the EBMTP (value of argument method), call to the function EBMTP.
EBMTP类，打印：打印方法返回一个对象的描述类EBMTP，test），包括样本的大小，测试的假设数，进行测试类型（参数值I型错误率（参数typeone值）（参数值，名义水平测试alpha）名称（参数值的EBMTPmethod），调用函数EBMTP。

In addition, this method produces a table with the class, mode, length, and dimension of each slot of the EBMTP instance.
此外，这种方法产生一个与每个插槽EBMTP实例类，模式，长度，尺寸表。

summary : summary method for EBMTP class, provides numerical summaries of the results of an EBMTP and returns a list with the following three components. 
摘要：摘要EBMTP类，方法提供一个EBMTP结果数值的总结，并返回列表以下三部分组成。参考

1. rejections: A data.frame with the number(s) of rejected hypotheses for the nominal Type I error rate(s) specified by the alpha argument of the function MTP. 
1。拒绝：拒绝假设名义alpha功能MTP参数指定的类型，我的错误率（S）（S）与数据框。参考

2. index: A numeric vector of indices for ordering the hypotheses according to first adjp, then rawp, and finally the absolute value of statistic (not printed in the summary). 
2。指数：指数订购的假设，根据一个数值向量adjp，然后rawp，最后的绝对价值statistic（不印在总结）。参考

3. summaries: When applicable (i.e., when the corresponding quantities are returned by MTP), a table with six number summaries of the distributions of the adjusted p-values, unadjusted p-values, test statistics, and parameter estimates.
3。摘要：适用时（即，当相应的数量由MTP返回），与调整后的六个月数量分布摘要带够值，未经调整的P级值，测试统计，参数估计表。

EBupdate : update method for EBMTP class, provides a mechanism to re-run the MTP with different choices of the following arguments - nulldist, alternative, typeone, k, q, alpha, smooth.null, bw, kernel, prior, keep.nulldist, keep.rawdist, keep.falsepos, keep.truepos, keep.errormat, keep.margpar. When evaluate is 'TRUE', a new object of class EBMTP is returned. Else, the updated call is returned. The EBMTP object passed to the update method must have either a non-empty rawdist slot or a non-empty nulldist slot (i.e., must have been called with either 'keep.rawdist=TRUE' or 'keep.nulldist=TRUE'). 
EBupdate：更新EBMTP类的方法，提供了一种机制不同选择以下参数重新运行中期计划 - nulldist，替代，typeone，K，Q，α，smooth.null，体重，内核之前，，keep.nulldist，keep.rawdist，keep.falsepos，keep.truepos，keep.errormat，keep.margpar。当评估为true，新的一类EBMTP的对象返回。否则，更新呼叫返回。 EBMTP对象传递给更新方法必须有一个非空的rawdist插槽或一个非空的nulldist槽（即，必须有被称为是keep.rawdist true或keep.nulldist = TRUE“）。参考

Additionally, when calling EBupdate for any Type I error rate other than FWER, the typeone argument must be specified (even if the original object did not control FWER). For example, typeone="fdr", would always have to be specified, even if the original object also controlled the FDR. In other words, for all function arguments, it is safest to always assume that you are updating from the EBMTP default function settings, regardless of the original call to the EBMTP function. Currently, the main advantage of the EBupdate method is that it prevents the need for repeated estimation of the test statistics null distribution. 
此外，当调用EBupdate任何类型的错误率比FWER，必须指定typeone参数（即使原来的对象没有控制FWER的）。例如，typeone="fdr"，总是要指定，即使原来的对象也控制了FDR。换句话说，函数的所有参数，它是最安全的，总是假设要更新EBMTP默认的功能设置，无论原来的呼叫EBMTP功能。目前，EBupdate方法的主要优点是，它可以防止反复的测试统计，空分布的估计需要。参考

To save on memory, if one knows ahead of time that one will want to compare different choices of bootstrap-based null distribution, then it is both necessary and sufficient to specify 'keep.rawdist=TRUE', as there is no other means of moving between null distributions other than through the non-transformed non-parametric bootstrap distribution. In this case, 'keep.nulldist=FALSE' may be used. Specifically, if an object of class EBMTP contains a non-empty rawdist slot and an empty nulldist slot, then a new null distribution will be generated according to the values of the nulldist= argument in the original call to EBMTP or any additional specifications in the call to update. On the other hand, if one knows that one wishes to only update an EBMTP object in ways which do not involve choice of null distribution, then 'keep.nulldist=TRUE' will suffice and 'keep.rawdist' can be set to FALSE (default settings). The original null distribution object will then be used for all subsequent calls to update. 
为了节省内存，如果一个人知道未来的时间，一会要比较不同的选择，引导为主的空分布，那么它是必要的和足够的指定“keep.rawdist = TRUE”，有没有其他办法移动之间通过非转化的非参数引导分布以外空分布。在这种情况下，“keep.nulldist = FALSE，”可使用。具体来说，如果一个对象的类EBMTP包含一个非空的rawdist插槽和一个空的nulldist槽，然后一个新的空分布将根据<X值产生>nulldist=或任何调用EBMTP在其他规格在原有的呼叫参数。另一方面，如果一个人知道一个愿望，只有更新的方式，不涉及空分布的选择，然后“keep.nulldist = TRUE就足够了，”keep.rawdist“update对象可以是设置EBMTP（默认设置）。然后将原来的空分布对象使用的所有后续调用FALSE。参考

N.B.: Note that keep.rawdist=TRUE is only available for the bootstrap-based resampling methods. The non-null distribution does not exist for the permutation or influence curve multivariate normal null distributions.
注：请注意，keep.rawdist=TRUE只为引导为主的重采样方法可用。非空分布不存在置换或影响曲线多元正常空分布。

ebmtp2mtp : coersion method for converting objects of class EBMTP to objects of class MTP. Slots common to both objects are taken from the object of class EBMTP and used to create a new object of class MTP. Once an object of class MTP is created, one may use the method update to perform resampling-based multiple testing (as would have been done with calls to MTP) without the need for repeated resampling.
ebmtp2mtp：coersion类转换对象方法EBMTP类MTP对象。两个对象的共同插槽取自对象类EBMTP和使用，以创建一个新的对象类MTP。一旦MTP类的对象被创建，而不需要重复使用的方法update执行重采样为基础的多个测试（已完成调用MTP）重采样。

作者（S）----------Author(s)----------

Houston N. Gilbert, based on the original <code>MTP</code> class and method definitions written by Katherine S. Pollard

参考文献----------References----------

hypothesis testing with applications to genomics: New developments in R/Bioconductor package multtest. Journal of Statistical Software (submitted). Temporary URL: http://www.stat.berkeley.edu/~houston/JSSNullDistEBMTP.pdf. 
discovery rate in multiple testing with independent statistics. J. Behav. Educ. Statist. Vol 25: 60-83. 
procedures that control the false discovery rate. Biometrika. Vol. 93: 491-507. 
http://www.bepress.com/sagmb/vol4/iss1/art29/ 

Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: Focus on the false discovery rate and simulation study. Biometrical Journal, 50(5):716-44. http://www.stat.berkeley.edu/~houston/BJMCPSupp/BJMCPSupp.html. 
graphical model selection with applications to biological networks. Technical report, U.C. Berkeley Division of Biostatistics Working Paper Series, April 2009. URL http://www.bepress.com/ucbbiostat/paper245. 

参见----------See Also----------

EBMTP, EBMTP-methods, MTP, MTP-methods, [-methods, as.list-methods, print-methods, plot-methods, summary-methods, mtp2ebmtp,
EBMTP，EBMTP-methods，MTP，MTP-methods，[-methods，as.list-methods，print-methods，plot-methods，summary-methods，mtp2ebmtp

举例----------Examples----------

## See EBMTP function: ? EBMTP[＃见EBMTP的功能：？ EBMTP]

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

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