R语言 cellHTS包 summarizeReplicates()函数中文帮助文档(中英文对照)

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summarizeReplicates(cellHTS)
summarizeReplicates()所属R语言包：cellHTS

                                        Summarizes between normalized replicate values given in a cellHTS object, obtaining a single z-score for each probe
                                         总结了规范化复制在cellHTS对象，为每个探针获得一个z得分值

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Summarizes the normalized (and possibly already scored) replicate values given in a cellHTS object, and calculates a single z-score value for each probe.
总结归（可能已经取得）cellHTS对象发出的复制值，并计算出一个单一的Z-得分为每个探针的价值。

Currently this function is implemented only for single-color data.
目前此功能只为单一颜色的数据。


用法----------Usage----------


summarizeReplicates(x, zscore, summary = "min")



参数----------Arguments----------

参数：x
a cellHTS object that has already been normalized (see details).
1 cellHTS对象已归（见详情）。


参数：zscore
indicates if the replicate values should be centered and scaled.  If missing (default), the data will not be centered and scaled. Otherwise, the value of this argument should be a character string, either "+" or "-", specifying the sign to use for the calculated  z-scores (see details).
表示，如果复制的值应居中和缩放。如果缺少（默认），数据不会被中心和缩放。否则，这个参数的值应该是一个字符串，无论是“+”或“ - ”，指定使用的符号计算Z-分数（见详情）。


参数：summary
a character string indicating how to summarize between replicated measurements.  One of "min" (default), "mean", "max", "rms", "closestToZero", or "FurthestFromZero" can be used (see details).
一个字符串，指示如何总结之间的复制测量。一个“分”（默认），“中庸”，“最大”，“RMS”，“closestToZero”，或“FurthestFromZero”可以使用（见详情）。


Details

详情----------Details----------

Given the normalized values given in the slot xnorm of x, a single z-score is calculated for each probe.
鉴于插槽中的标准化值xnormx，Z-分数计算每个探针。

The argument zscore indicates the state of the normalized replicate measurements: if zscore is missing, it is assumed that the replicates have been scored, by calling normalizePlates  with the argument zscore equal to "-" or "+"; Otherwise, zscore should be given, so that a robust z-score  is calculated for each plate and each well by subtracting the overall median and dividing by the overall mad. The overall median and mad are taken by considering the distribution of intensities (over all plates) in the wells whose content is annotated as sample.  The allowed values for zscore ("+" or "-") are used to set the sign of  the calculated z-scores. For example, with a zscore="-" a strong decrease in the signal will be represented  by a positive z-score, whereas setting zscore="+",  such a phenotype will be represented by a negative z-score.   This option can be set to calculate the results to the commonly used convention.
参数zscore表示归重复测量的状态：如果zscore缺少，它被认为已经取得的复制调用normalizePlates参数zscore等于“ - ”或“+”，否则，zscore应该得到这样一个强大的Z-分数计算，减去整体中位数除以整体，每个板块，每口井疯了。整体中位数和疯狂是被考虑的强度分布（超过所有板），其内容是sample注明的井。允许值zscore（“+”或“ - ”）是用于设置计算Z-分数的迹象。例如，zscore="-"在信号强的减少将代表积极Z-得分，而设置zscore="+"，这样的表型将负的Z-分数表示。此选项可以设置常用的“公约”的计算结果。

Finally, a single z-score per probe is calculated by summarizing between scored replicates. If summary="mean", the average of replicate values is considered; if  summary="max", then the maximum of replicate intensities is taken; if summary="min", the minimum is considered, instead (conservative); if summary="rms", the square root of the mean squared value of the replicates (root mean square) is taken as a summary function; if summary="closestToZero", the value closest to zero is taken as a summary (ueful when both sides of the distribution of z-score values are of interest); if summary="furthestFromZero", the value furthest from zero is taken as a summary (ueful when both sides of the distribution of z-score values are of interest)
最后，每个探针一个单一的Z-分数计算总结之间刻痕复制。如果summary="mean"，然后复制强度最大;如果summary="max"，被认为是重复值的平均值;如果summary="min"如果被认为是最低，而不是（保守）; summary="rms"，平方根的平均平方值（均方根）的复制，是作为一个汇总函数; summary="closestToZero"如果，接近零值摘要（ueful时，双方Z-分数的分布值是利息）;如果summary="furthestFromZero"，从零最远的价值为摘要（ueful的是Z-得分值的分布时，双方的利益）


值----------Value----------

An object of class cellHTS, which is a copy of the argument x plus the slot score, a numeric vector containing the z-factor for each well in every plate. The length of this vector is therefore equal to the product between the plateSize and the number of plates. Moreover, the processing status of the cellHTS object is updated
一个类的对象cellHTS，这是一个参数的副本x加上插槽score，数字向量，每口井，每板含有z因子。因此，这个向量的长度等于产品的之间的plateSize的板数。此外，处理cellHTS对象的状态更新


作者（S）----------Author(s)----------


W. Huber <a href="mailto:huber@ebi.ac.uk">huber@ebi.ac.uk</a>, Ligia Braz <a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>



参见----------See Also----------

normalizePlates, summarizeChannels
normalizePlates，summarizeChannels


举例----------Examples----------


    data(KcViabSmall)
    x <- normalizePlates(KcViabSmall, normalizationMethod="median")
    x <- summarizeReplicates(x, zscore="-", summary="min")

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


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