summarizeChannels(cellHTS2)
summarizeChannels()所属R语言包：cellHTS2
Summarization of dual-channel data
双通道数据综述
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Combines plate intensities (raw or already corrected in a per-plate fashion) from multi-channel data stored in slot assayData of a cellHTS instance by applying the function defined in fun.
结合板强度（原料或已在每一个板块的时尚纠正）从多通道数据存储在插槽assayDatacellHTS应用fun定义的函数的实例。
用法----------Usage----------
summarizeChannels(object,
fun = function(r1, r2, thresh=-Inf) ifelse(r1>thresh, r2/r1, as.numeric(NA)))
参数----------Arguments----------
参数：object
an object of class cellHTS that has been configured. See details.
cellHTS类的对象已配置。查看详情。
参数：fun
a user-defined function for the multi channel summarization. fun takes as many numeric vectors as there are channels, names r1, r2, etc., and returns a single numeric vector of the same length. The default is to take the 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.
为多渠道汇总的用户定义函数。 fun需要尽可能多的数字向量，有渠道，名r1, r2, etc.，并返回一个单一的数字相同长度的向量。默认情况下是采取第二和第一通道之间的比例，与阈值，r1以上的部分，应当由用户设置使用。
Details
详情----------Details----------
For each plate and replicate of a multi-color experiment, the function defined in fun is applied to relate the intensity values in the respective channels of the cellHTS object. The default is to take the ratio between the second and first channels, with a threshold on r1 (see the Usage section). This threshold should be adjusted by the user according to the data. For an example, see the Examples section. This function uses the content of slot assayData of object and can be applied either to raw data or after per-plate correction of the intensity values in each channel using function normalizePlates. This choice depends on channel summarization method that one intends to apply (i.e., the function given by argument fun).
对于一个多色彩的实验，在funcellHTS对象各自的渠道与强度值定义的函数每块板和复制。默认是r1（见“用法”部分）的阈值，采取第二和第一通道之间的比率。此阈值应根据数据，由用户调整。举一个例子，请参见“示例”部分。此功能使用的插槽assayDataobject的内容，并可以应用于原始数据或每板在每个通道的强度，使用功能normalizePlates值的校正后。这个渠道汇总方法的选择取决于一个打算申请（即由参数给定的功能fun）。
值----------Value----------
An object of class cellHTS with the summarized multi-channel intensities stored in slot assayData. This is an object of class assayData containing one matrix with the summarized channel data (dimensions nrFeatures x nrSamples).
一个类的对象cellHTS存储插槽assayData汇总多渠道的强度。这是一个类的对象assayData汇总通道数据（尺寸nrFeatures x nrSamples）含有一个矩阵。
作者（S）----------Author(s)----------
Ligia Bras <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>
参考文献----------References----------
参见----------See Also----------
normalizePlates, scoreReplicates, summarizeReplicates.
normalizePlates，scoreReplicates，summarizeReplicates。
举例----------Examples----------
data(dualCh)
x <- dualCh
table(wellAnno(x))
## Define the controls for the different channels:[＃定义为不同的渠道控制：]
negControls=vector("character", length=dim(Data(x))[3])
## 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$"
posControls = vector("character", length=dim(Data(x))[3])
## channel 1 - no controls[1＃通道 - 无控制]
## channel 2 - geneC and geneD[＃2通道 - geneC和geneD]
posControls[2]="(?i)^geneC$|^geneD$"
## Not run: [＃无法运行：]
writeReport(cellHTSlist=list("raw"=x), map=TRUE, plotPlateArgs=TRUE, posControls=posControls, negControls=negControls)
## End(Not run)[＃结束（不运行）]
## In this example, we first normalize each channel separately by [＃在这个例子中，我们首先规范每个通道分别由]
## plate median scaling (no variance adjustment), since we need to make the measurements [＃板中位数比例（无差异调整），因为我们需要做的测量]
## comparable across plates for the next step of channel summarization:[＃可比跨板为下一步的通道概括：]
xn = normalizePlates(x, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")
## Then, we define a low intensity threshold for the measurements in the constitutive channel R1, [＃然后，我们定义为低强度阈值的测量构通道R1，]
## which will be set to the 5% quantile of the overall plate median corrected intensities in R1, [＃将整体板块中位数纠正R1强度设置为5％的分量，]
## and take the ratio R2/R1.[＃采取比R2/R1。]
xn = summarizeChannels(xn, fun = function(r1, r2,
thresh=quantile(r1, probs=0.05, na.rm=TRUE)) ifelse(r1>thresh, r2/r1, as.numeric(NA)))
## After channel summarization, we take the log2 and apply plate median normalization, [＃通道汇总后，我们采取的log2和应用板中位数标准化，]
## and opt to not adjust the variance:[＃选择不调整方差：]
xn = normalizePlates(xn, scale="multiplicative", log=TRUE, method="median", varianceAdjust="none")
## Define the controls for the normalized and summarized intensities (only one channel):[＃定义的规范化和归纳强度（只有一个通道）的控制：]
negControls = vector("character", length=dim(Data(xn))[3])
## For the single channel, the negative controls are geneA and geneB [＃对于单通道，阴性对照的是geneA和geneB]
negControls[1]= "(?i)^geneA$|^geneB$"
posControls = vector("character", length=dim(Data(xn))[3])
## For the single channel, the negative controls are geneC and geneD [＃对于单个通道阴性对照geneC的和geneD]
posControls[1]="(?i)^geneC$|^geneD$"
## Not run: [＃无法运行：]
writeReport(cellHTSlist=list("raw"=x, "normalized"=xn), force=TRUE, map=TRUE, plotPlateArgs=list(xrange=c(-3,3)),
posControls=posControls, negControls=negControls)
## End(Not run)[＃结束（不运行）]
## Another option could be to just take the log2 of the ratio between R2 and R1 raw intensities:[＃另一种选择可能只是采取的log2 R2和R1的原料强度之间的比率：]
xn1 = summarizeChannels(x, fun = function(r1, r2) log2(r2/r1))
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 14:19:04
