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

loveR · 发表于 2012-2-26 07:39:39

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

 Class "MTP", classes and methods for multiple testing procedure output
 “中期计划”的类，类和多个测试程序输出的方法

 译者：生物统计家园网机器人LoveR

描述----------Description----------

An object of class MTP is the output of a particular multiple testing procedure, for example, generated by the MTP function. It has slots for the various data used to make multiple testing decisions, such as adjusted p-values and confidence regions.
中期计划类的对象是一个特定的多个测试程序的输出，例如，由MTP功能的产生。它有插槽，用来做多个测试决定的各种数据，如调整后的P-值和置信区域。

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 conf.reg = ...., object of class array cutoff = ...., object of class matrix 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 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 = ......，对象类数字参考conf.reg = ...，对象类数组参考截止= ......，类矩阵参考对象拒绝......，对象类矩阵参考rawdist = ......，对象类矩阵参考nulldist = ...，对象的类矩阵参考nulldist.type = ...，阶级性参考marg.null对象= ......，阶级性参考marg.par对象。，对象类矩阵参考标签= ......，对象类数字参考指数= ......，对象类矩阵参考呼叫= ......，调用类的对象参考的种子......，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。

conf.reg For the test of single-parameter null hypotheses using t-statistics (i.e., not the F-tests), the numeric array of lower and upper simultaneous confidence limits for the parameter vector, for each value of the nominal Type I error rate alpha (computed only if the get.cr argument is TRUE).
conf.reg对于单参数的空假设使用t-统计量（即F检验），数字数组上下同时置信限参数向量的名义类型的每个值测试我的错误率alpha（get.cr参数计算只有为TRUE）。

cutoff The numeric matrix of cut-offs for the vector of test statistics for each value of the nominal Type I error rate alpha (computed only if the get.cutoff argument is TRUE).
cutoff截止权衡的我错误率alpha（get.cutoff参数计算仅是TRUE）的名义类型的每个值的向量测试统计的数字矩阵。

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); option not currently available for permutation null distribution, i.e., nulldist='perm'). 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（返回只有keep.nulldist=TRUE）;置换空分布，即目前没有可用的选项，nulldist='perm'）。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', 'ic', or 'perm'.
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”，“IC”，或“烫发”的呼叫参数值之一。

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。

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 MTP 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，当一个人要更新中期计划的对象，使用默认的F-统计marg.null和marg.par设置nulldist='boot.qt'。

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 = "MTP") 
signature(x = "MTP")参考

[ : Subsetting method for MTP class, which operates selectively on each slot of an MTP instance to retain only the data related to the specified hypotheses.
[：MTP类，经营选择性MTP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 MTP 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MTPlist，每个插槽的条目。

plot : plot methods for MTP class, produces the following graphical summaries of the results of a MTP. The type of display may be specified via the which argument. 
图：图MTP类，方法产生一个中期计划的结果，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

5. Plot of confidence regions for user-specified parameters, by default the 10 parameters corresponding to the smallest adjusted p-values (argument top). 
5。图信心区域用户指定的参数，默认情况下，最小的调整p值对应的10个参数（参数top）。参考

6. Plot of test statistics and corresponding cut-offs (for each value of alpha) for user-specified hypotheses, by default the 10 hypotheses corresponding to the smallest adjusted p-values (argument top). 
6。默认情况下，相应的最小的调整p值10假设检验统计量和相应的截止权衡（每个alpha值）为用户指定的假说，图（参数top）。参考

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.
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 MTP class, returns a description of an object of class MTP, 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 MTP (value of argument method), call to the function MTP.
MTP类，打印：打印方法返回一个对象的描述类MTP，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alphamethod），中期计划的名称（参数值），调用函数MTP。

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

summary : summary method for MTP class, provides numerical summaries of the results of a MTP and returns a list with the following three components. 
摘要：摘要MTP类的方法提供了一个中期计划的结果的数值汇总，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. (NULL values are returned if all three arguments get.cr, get.cutoff, and get.adjp are FALSE). 
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。（返回空值，如果所有三个参数get.cr，get.cutoff，get.adjp都是假的）。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。

update : update method for MTP class, provides a mechanism to re-run the MTP with different choices of the following arguments - nulldist, alternative, typeone, k, q, fdr.method, alpha, smooth.null, method, get.cr, get.cutoff, get.adjp, keep.nulldist, keep.rawdist, keep.margpar. When evaluate is 'TRUE', a new object of class MTP is returned. Else, the updated call is returned. The MTP 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'). 
更新：更新MTP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，fdr.method，α，smooth.null，方法，get.cr，get.cutoff，get.adjp，keep.nulldist，keep.rawdist，keep.margpar。当评估为true，新的中期计划类对象被返回。否则，更新呼叫返回。 MTP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

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 MTP 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 MTP or any additional specifications in the call to update. On the other hand, if one knows that one wishes to only update an MTP 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MTP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MTP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MTP（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。

mtp2ebmtp : coersion method for converting objects of class MTP to objects of class EBMTP. Slots common to both objects are taken from the object of class MTP and used to create a new object of class EBMTP. Once an object of class EBMTP is created, one may use the method EBupdate to perform resampling-based empirical Bayes multiple testing without the need for repeated resampling.
mtp2ebmtp：coersion类转换对象方法MTP类EBMTP对象。两个对象的共同插槽取自对象类MTP和使用，以创建一个新的对象类EBMTP。一旦EBMTP类的对象创建，可以使用EBupdate来执行，而不需要反复重新取样重采样为基础的经验Bayes多个测试方法。

作者（S）----------Author(s)----------

Katherine S. Pollard and Houston N. Gilbert with design contributions from Sandrine Dudoit and Mark J. van der Laan.

参考文献----------References----------

http://www.bepress.com/sagmb/vol3/iss1/art15/
http://www.bepress.com/sagmb/vol3/iss1/art14/
http://www.bepress.com/sagmb/vol3/iss1/art13/
http://www.bepress.com/ucbbiostat/paper121
http://www.bepress.com/sagmb/vol5/iss1/art14/

参见----------See Also----------

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

举例----------Examples----------

## See MTP function: ? MTP[＃见中期计划的功能：？中期计划]

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

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