R语言 cellHTS2包 scoreReplicates()函数中文帮助文档(中英文对照)

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scoreReplicates(cellHTS2)
scoreReplicates()所属R语言包：cellHTS2

                                        Scores normalized replicate values given in a cellHTS object
                                         分数归的复制在cellHTS对象给定值

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This function scores the normalized replicate values stored in slot assayData of a cellHTS object. Current available options are to take the z-score value or the per-replicate normalized percent inhibition (NPI). Data are stored in slot assayData overridding its current content.
此功能评分插槽中存储的值归复assayDatacellHTS对象。当前可用的选项是采取Z-得分值或每复制标准化％抑制（NPI）。数据存储在插槽assayData的overridding其当前内容。


用法----------Usage----------


scoreReplicates(object, sign="+", method="zscore", ...)



参数----------Arguments----------

参数：object
an object of class cellHTS that has already been normalized.
cellHTS类的对象已经标准化。


参数：sign
a character string, either "+" (default) or "-", which corresponds to multiplying the data by +1 or -1, respectively, after applying the scoring method specified by argument method. See details.
一个字符串，无论是“+”（默认）或“ - ”，以乘以+1或-1，分别在应用参数指定的计分法，数据对应 method。查看详情。


参数：method
a character string indicating which method to use to score the replicate measurements. Available options are "none", "zscore" (default), "NPI". See details.
一个字符串，指示要使用哪种方法将比分复制测量。可用的选项是“无”，“zscore”（默认），“非营利机构”。查看详情。


参数：...
additional parameters required by some of the methods chosen in method.
一些选择的方法，在method需要额外的参数。


Details

详情----------Details----------

This function scores the normalized values given in the slot assayData of object. Current availabe scoring methods are:
此功能评分在槽的标准化值assayDataobject。当前速效评分方法是：

method="none", no scoring is applied.
method="none"应用，没有得分。

method="zscore" (robust z-scores), for each replicate, this is calculated by subtracting the overall median from each measurement and dividing the result by the overall mad. These are estimated for each replicate by considering the distribution of intensities (over all plates) in the wells whose content is annotated as sample.
method="zscore"（强大的Z-分数），每个重复，这是由减去每次测量的整体中位数除以整体mad结果计算。这些估计每个重复考虑的强度分布（超过所有板），其内容是sample注明的井。

method="NPI" (normalized percent inhibition applied in a per-replicate basis, i.e. using the overall mean of positive and negative controls across all plates of a given replicate), for each replicate, this method consists of subtracting each measurement from the average of the intensities on the positive controls (taken across all plates), and this result is then divided by the difference between the averages of the measurements on the positive and the negative controls (taken across all plates). If this method is chosen, one may need to provide further arguments to scoreReplicates, namely, arguments posControls and negControls. These arguments should be vectors of regular expression patterns specifying the name of the positive(s) and negative(s) controls, respectivey, as provided in the plate configuration file. The length of these vectors should match the current number of channels in object (i.e. dim(Data(object))[3]). By default, if posControls or negControls are not given, pos and neg will be taken as the name for the wells containing positive or negative controls. The content of posControls and negControls is passed to regexpr for pattern matching within the well annotation given in the featureData slot of object (which can be accessed via wellAnno(object)) (see examples for summarizeChannels).
method="NPI"（的标准化％抑制应用在每一个复制的基础上，即使用阳性和阴性对照，在一个给定的复制的所有板块的整体平均）为每个复制，这种方法由减去平均每个测量阳性对照（所有板块），这一结果是积极测量的平均值和阴性对照组（所有板块）之间的差异分为强度。如果选择这种方法，可能需要提供进一步的论据scoreReplicates，即参数posControls和negControls。这些参数应该是正则表达式模式（S）（S）的积极和消极的控制，respectivey板配置文件中提供的名称指定的向量。这些向量的长度应符合渠道object（即dim(Data(object))[3]）。默认情况下，如果posControls或negControls不给，POS和NEG将采取积极或消极的控制井的名称。 posControls和negControlsregexprfeatureDataobject（这可通过插槽以及注释内的模式匹配通过的内容wellAnno(object)）（看到summarizeChannels）。

After replicate scoring using the chosen method, the value given in sign ("+" or "-") is used to set the sign of the calculated scores.  For example, with a sign="-", a strong decrease in the signal will be represented  by a positive score, whereas setting sign="+", such a phenotype will be represented by a negative score. This option can be set to calculate the results to the commonly used convention.
重复使用所选择的方法得分后，在给定的值sign（“+”或“ - ”）是用于设置计算分数的迹象。例如，sign="-"，在信号强的下降将代表积极得分，而设置sign="+"，这样的表型将代表一个负分。此选项可以设置常用的“公约”的计算结果。


值----------Value----------

A cellHTS object with its slot assayData replaced with the scored values (same dimension).
一个cellHTS其槽assayData对象的得分值（相同尺寸）取代。

Important: Note that the processing state "scored" of the cellHTS object is only updated to TRUE after summarizing the replicates, which is the next preprocessing step (see summarizeReplicates).
重要：请注意，处理状态“拿下”cellHTS对象只更新后总结的复制，这是未来的预处理步骤（见TRUEsummarizeReplicates）。


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>



参考文献----------References----------



参见----------See Also----------

normalizePlates, summarizeChannels, summarizeReplicates.
normalizePlates，summarizeChannels，summarizeReplicates。


举例----------Examples----------


    data(KcViabSmall)
    x <- normalizePlates(KcViabSmall, scale="multiplicative", method="median", varianceAdjust="none")
    x <- scoreReplicates(x, sign="-", method="zscore")
    x &lt;- summarizeReplicates(x, summary="min") # conservative approach[保守的方法]

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


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