summarizeChannels(cellHTS)
summarizeChannels()所属R语言包：cellHTS
Normalization and transformation of dual-channel data
双通道数据的标准化和改造
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Normalizes and/or transforms dual-channel data xraw of a cellHTS object by applying the function defined in fun.
标准化和/或转换双通道的数据xrawcellHTS应用fun定义的函数对象。
用法----------Usage----------
summarizeChannels(x,
fun = function(r1, r2, thresh) ifelse(r1>thresh, log2(r2/r1), as.numeric(NA)),
adjustPlates, zscore, ...)
参数----------Arguments----------
参数：x
a cellHTS object that has been configured.
cellHTS已配置的对象。
参数：fun
a user-defined function for the two channel summarization. fun takes two numeric vectors and returns a numeric vector of the same length. The default is to take the log2-ratio between the second and first channels, with a threshold on r1 shown above in the Usage section that should be set by the user.
用户定义函数的两个通道的总结。 fun需要两个数值向量，并返回一个同样长度的数字向量。默认是采取的log2率与阈值之间的第二和第一的渠道，r1以上的部分，应当由用户设置使用。
参数：adjustPlates
scalar character string indicating the normalization method to apply to adjust for plate-to-plate variations (and possibly well-to-well variations). This is done before applying fun. Allowed values are "median", "mean", "shorth", "POC", "NPI", "negatives" and Bscore. If adjustPlates is missing (the default), no plate-wise correction will be performed.
标字符串，指示板到板的变化（以及可能的变化以及对井）申请调整的规范化方法。这是申请fun之前。允许的值是"median"，"mean"，"shorth"，"POC"，"NPI"，"negatives"和Bscore。如果adjustPlates丢失（默认），将执行无板明智的校正。
参数：zscore
indicates if the z-scores should be determined after normalization and transformation. If missing (default), the data will not be scored. Otherwise, it should be a character string, either "+" or "-", specifying the sign to use for the z-scores.
表示，如果Z-分数应标准化和改造后确定。如果失踪（默认），数据不会被拿下。否则，它应该是一个字符串，无论是“+”或“ - ”，指定使用Z-分数的迹象。
参数：...
Further arguments that get passed on to the function implementing the normalization method chosen by adjustPlates. See the Details section and the normalizePlates function.
进一步的参数被传递到功能实现标准化的方法adjustPlates选择。看到细节部分和normalizePlates功能。
Details
详情----------Details----------
For each plate and replicate of a two-color experiment, the function defined in fun is applied to relate the intensity values in the two channels of the cellHTS object. The default is to take the log2-ratio between the second and first channels, with a threshold on r1 (see the Usage section). This threshold should be ajusted by the user according to the data. For an example, see the Examples section.
对于每块板和两色的实验复制，fun定义的功能适用于涉及在cellHTS对象的两个通道的强度值。默认是r1（见“用法”部分）的阈值，之间的log2比第二和第一的渠道。此阈值应根据用户的数据ajusted。举一个例子，请参见“示例”部分。
If adjustPlates is not missing, the values for each channel will be corrected for plate effects before applying fun, by considering the chosen normalization method. The available options are adjustPlates="median" (median scaling), adjustPlates="mean" (mean scaling), adjustPlates="shorth" (scaling by the midpoint of the shorth), adjustPlates="POC" (percent of control), adjustPlates="negatives" (scaling by the average on the negative controls), adjustPlates="NPI" (normalized percent inhibition) and adjustPlates="Bscore" (B score method). For more details about these normalization options, please refer to normalizePlates. By default, adjustPlates is missing.
如果adjustPlates不缺，每个通道的值将板效应纠正前申请fun，考虑选择的归一化法。可用的选项adjustPlates="median"（位数缩放），adjustPlates="mean"（缩放），adjustPlates="shorth"（通过的shorth中点缩放），adjustPlates="POC"（％）的控制， adjustPlates="negatives"（阴性对照平均缩放），adjustPlates="NPI"（归抑制％）和adjustPlates="Bscore"（B评分法）。对于这些标准化选项的更多细节，请参考normalizePlates。默认情况下，adjustPlates丢失。
If zscore is not missing, a robust z-score is calculated based on the channel-summarized measurements. The z-score for each individual measurement will be determined for each plate and each well by subtracting the overall median and dividing by the overall mad. The allowed values for zscore ("+" or "-") are used to set the sign of the calculated z-scores. See summarizeReplicates for more details.
zscore如果不缺，一个强大的Z-分数计算上的通道汇总测量。为每个测量Z-得分，将被确定为每块板，每口井减去整体median和除以整体mad。允许值zscore（“+”或“ - ”）是用于设置计算Z-分数的迹象。看到summarizeReplicates更多细节。
值----------Value----------
An object of class cellHTS, which is a copy of the argument x, plus an additional slot xnorm containing the normalized data. This is an array of the same dimensions as xraw, except in the dimension corresponding to the number of channels, since the two-channel intensities have been combined into one intensity value.
cellHTS类的对象，这是一个参数的副本x，加上一个额外的插槽xnorm包含规范化的数据。这是数组xraw，除了在尺寸相应的通道数量，因为双通道强度已合并成一个强度值相同的尺寸。
Moreover, the processing status of the cellHTS object is updated in the slot state to x$state["normalized"]=TRUE.
此外，处理cellHTS对象的状态更新插槽statex$state["normalized"]=TRUE。
Additional outputs may be given if adjustPlates="Bscore". Please refer to the help page of the Bscore function.
如果adjustPlates="Bscore"可给予额外的产出。 Bscore函数，请参阅帮助页面。
作者（S）----------Author(s)----------
Ligia Braz <a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>, Wolfgang Huber <a href="mailto:huber@ebi.ac.uk">huber@ebi.ac.uk</a>
参见----------See Also----------
normalizePlates, Bscore, summarizeReplicates
normalizePlates，Bscore，summarizeReplicates
举例----------Examples----------
## Not run: [＃无法运行：]
datadir <- system.file("DualChannelScreen", package = "cellHTS")
x <- readPlateData("Platelist.txt", "TwoColorData", path=datadir)
x <- configure(x, "Plateconf.txt", "Screenlog.txt", "Description.txt", path=datadir)
table(x$wellAnno)
## Define the controls for the different channels:[＃定义为不同的渠道控制：]
negControls=vector("character", length=dim(x$xraw)[4])
## channel 1 - gene A[1＃通道 - 一个基因]
## case-insensitive and match the empty string at the beginning and end of a line (to distinguish between "geneA" and "geneAB", for example, although this is not a problem for the well annotation in this example)[＃不区分大小写，匹配空字符串的开始和结束行（区分“geneA”和“geneAB”，例如，虽然这不是一个问题，在这个例子很好注释）]
negControls[1]= "(?i)^geneA$"
## channel 2 - gene A and geneB[2＃通道 - 基因A和geneB]
negControls[2]= "(?i)^geneA$|^geneB$"
posControls = vector("character", length=dim(x$xraw)[4])
## channel 1 - no controls[1＃通道 - 无控制]
## channel 2 - geneC and geneD[＃2通道 - geneC和geneD]
posControls[2]="(?i)^geneC$|^geneD$"
writeReport(x, posControls=posControls, negControls=negControls)
## In this example, we first normalize each channel separately by plate median scaling. [＃在这个例子中，我们首先规范每个通道分别由板块中位数缩放。]
## Then, we define a low intensity threshold for the measurements in the constitutive channel R1, [＃然后，我们定义为低强度阈值的测量构通道R1，]
## which will be set to the 5[＃将被设置为5]
x = summarizeChannels(x, fun = function(r1, r2,
thresh=quantile(r1, probs=0.05, na.rm=TRUE)) ifelse(r1>thresh, log2(r2/r1), as.numeric(NA)),
adjustPlates="median")
## Note that the plate median scaling is applied to each channel, prior to channel summarization.[＃注意该板块中缩放适用于每个通道前，通道总结。]
## Define the controls for the normalized intensities (only one channel):[定义归强度（只有一个通道）的控制：]
negControls = vector("character", length=dim(x$xnorm)[4])
## For the single channel, the negative controls are geneA and geneB [＃对于单通道，阴性对照的是geneA和geneB]
negControls[1]= "(?i)^geneA$|^geneB$"
posControls = vector("character", length=dim(x$xnorm)[4])
## For the single channel, the negative controls are geneC and geneD [＃对于单个通道阴性对照geneC的和geneD]
posControls[1]="(?i)^geneC$|^geneD$"
writeReport(x, force=TRUE, plotPlateArgs=list(xrange=c(-3,3)),
posControls=posControls, negControls=negControls)
## End(Not run)[＃结束（不运行）]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 14:22:22
