MTP-methods(multtest)
MTP-methods()所属R语言包：multtest
Methods for MTP and EBMTP objects in Package ‘multtest’
方法MTP和EBMTP对象包multtest
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Summary, printing, plotting, subsetting, updating, as.list and class conversion methods were defined for the MTP and EBMTP classes. These methods provide visual and numeric summaries of the results of a multiple testing procedure (MTP) and allow one to perform some basic manipulations of objects class MTP or EBMTP. <br>
被定义为MTP和EBMTP类汇总，打印，绘图，子集，更新，as.list和类转换方法。这些方法提供了多个测试程序（MTP）的结果的可视化和数字摘要，并允许一个对象类MTP或EBMTP执行一些基本操作。参考
Several of the methods with the same name will work on objects of their respective class. One exception to this rule is the difference between update and EBupdate (described below). Because of the differences in the testing procedures, separately named methods were chosen to clearly delineate which method was being applied to which type of object.
几个具有相同名称的方法，将工作在各自的类的对象。这个规则的一个例外是update和EBupdate（如下所述）之间的差异。因为在测试程序的不同，分别命名方法选择，清楚地界定哪些方法被应用到该类型的对象。
方法----------Methods----------
[ : Subsetting method for MTP and EBMTP classes, which operates selectively on each slot of an MTP or EBMTP instance to retain only the data related to the specified hypotheses.
：MTP和EBMTP类，经营选择性的每个插槽的子集方法MTP或EBMTP实例，只保留到指定的假说有关的数据。
as.list : Converts an object of class MTP or EBMTP to an object of class list, with an entry for each slot.
as.list：类MTP或EBMTP对象类的一个对象转换list，每个插槽的条目。
plot : plot methods for MTP and EBMTP classes, produces the following graphical summaries of the results of a MTP. The type of display may be specified via the which argument. <br>
图：MTP和EBMTP类，图的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. <br>
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. <br>
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). <br>
3。调整后的P-值与测试统计散点图（又称火山图）。参考
4. Plot of unordered adjusted p-values. <br>
4。图的无序调整的p值。参考
Only for objects of class MTP: <br>
只有类MTP对象：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). <br>
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). <br>
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
Plots (5) and (6) are not available for objects of class EBMTP because the function EBMTP returns only adjusted p-values and not confidence regions of cut-offs. 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.
图（5）和（6）是不是类对象EBMTP因为功能EBMTP返回只调整p值，而不是截止取舍的信心区域。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 and EBMTP classes, returns a description of an object of either class, 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 or EBMTP.
打印：打印MTP和EBMTP类，方法返回描述的任一类的对象，包括样本大小，测试的假设数，进行测试类型（参数值test ），I类错误率（参数typeone），测试的名义水平（参数值的价值alpha），中期计划的名称（参数method），呼吁值MTP或EBMTP的功能。
In addition, this method produces a table with the class, mode, length, and dimension of each slot of the MTP or EBMTP instance.
此外，这种方法产生的每个插槽MTP或EBMTP实例类，模式，长度，和维表。
summary : summary method for MTP and EBMTP classes, provides numerical summaries of the results of a MTP and returns a list with the following three components. <br>
摘要：总结MTP和EBMTP类，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 or EBMTP. (For objects of class MTP, NULL values are returned if all three arguments get.cr, get.cutoff, and get.adjp are FALSE). <br>
1。拒绝：拒绝假设为我的错误率（S）由alpha参数的功能MTP或EBMTP指定标称类型（S）的数据框。 （对于类对象MTP，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). <br>
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 or EBMTP), 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：当适用（即返回MTP或EBMTP），用半年的调整后的P-值的分布数量汇总，未经调整的P级值，测试统计表时，相应的数量和参数估计。
update : update methods for MTP class, respectively, 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').<br>
更新：MTP类，分别更新方法提供了一种机制来重新运行的不同选择以下参数的中期计划 - 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
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').<br>
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. <br>
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 MTP or 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 (EB)MTP or any additional specifications in the call to (EB)update. On the other hand, if one knows that one wishes to only update an (EB)MTP object in ways which do not involve choice of bootstrap 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. <br>
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，如果一个类的对象MTP或EBMTP包含一个非空的rawdist插槽和一个空的nulldist槽，然后将产生一个新的空分布，根据nulldist=参数值在原来的呼叫(EB)MTP或任何调用(EB)update在其他规格。另一方面，如果一个人知道一个愿望只更新(EB)MTP的方式不涉及引导空分布的选择，然后keep.nulldist = TRUE就足够了，“keep.rawdist对象，设置FALSE（默认设置）。然后将原来的空分布对象使用的所有后续调用update。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。
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)----------
Katherine S. Pollard and Houston N. Gilbert with design contributions from Sandrine Dudoit and Mark J. van der Laan.
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
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发表于 2012-2-26 07:39:48
