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

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meeboQuality(arrayQuality)
meeboQuality()所属R语言包：arrayQuality

                                        Diagnostics plots designed for MEEBO set controls
                                         Meebo的一套控制设计，诊断图

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This component generates several exploratory plots customized to the various types of controls provided in the MEEBO set. All results are saved as an image. Tested on GenePix format only (11-18-2005). For more details about the plots, please refer to the HTML description.
这个组件生成定制控制在Meebo的集提供的各类探索图。所有的结果都保存为一个图像。 GenePix格式（11-18-2005）上进行测试。对于图的更多细节，请参阅HTML描述。


用法----------Usage----------


meeboQuality(fnames = NULL, path = ".", galfile = NULL, source
="genepix.median", other.columns = c("Flags"),controlMatrix=MeeboSpotTypes,controlId = c("ID", "Name"),
DOPING = TRUE,meeboSetQC = TRUE, SpotTypeFile = NULL, SpikeTypeFile =
NULL, cy3col = "CY3.ng._MjDC_V1.7", cy5col = "CY5.ng._MjDC_V1.7", id =
"SeqID", namecol = c("Symbol", "Name"), annot = NULL, bgMethod = "none", normMethod =
"p", diagnosticPlot = TRUE, output = TRUE, resdir = ".", dev = "png", organism = "Mm", DEBUG = FALSE,
...)



参数----------Arguments----------

参数：fnames
A "character" string naming the input files.
一个“字符”字符串，命名输入文件。


参数：path
A "character" string representing the data directory.  By default this is set to the current working directory (".").
一个“字符”字符串表示的数据目录。默认情况下，这是设置为当前工作目录（“。”）。


参数：galfile
A "character" string naming the file descrining the layout of the array. If missing, meeboQuality will read the layour from the gpr file.
一个“字符”命名的文件descrining阵列的布局的字符串。如果丢失，将meeboQuality阅读layour从GPR文件。


参数：source
A "character" string specifing the image analysis program which produced the output files. See ?read.maimages in package limma for more details.
一个“字符”字符串specifing图像分析程序产生的输出文件。有关详细信息，看到了什么？在包limma read.maimages。


参数：other.columns
See ?read.maimages in package limma for more details.
有关详细信息，看到了什么？在包limma read.maimages。


参数：controlMatrix
A character matrix of n by 2 or more columns. One column should contain a few regular expression of spotted probe sequences and another column should contain the corresponding control status. By default, controlMatrix is set to MeeboSpotTypes.
n字符由2个或更多列的矩阵。一列应该包含几个正则表达式的斑点探针序列和另一列应包含相应的控制状态。默认情况下，controlMatrix设置到MeeboSpotTypes。


参数：controlId
Character string. Name of the column of the gpr file used to define controls.
字符串。 GPR文件用来定义控件的列名称。


参数：DOPING
Logical. If 'TRUE', doping controls quality plots are generated.
逻辑。如果“TRUE”，兴奋剂控制质量图产生。


参数：meeboSetQC
Logical. If 'TRUE', mismatch and tiling controls quality plots are generated.
逻辑。如果产生了“TRUE”，不匹配和切片控制质量图。


参数：SpotTypeFile
A "character" string representing the name of the file containing spot type description for the array.
一个“人物”代表包含专为数组类型说明的文件名称的字符串。


参数：SpikeTypeFile
A "character" string representing the name of the file containing doping control information. See HTML description for more details.
一个“字”代表的含兴奋剂控制信息的文件名称的字符串。详情请参阅HTML描述。


参数：cy3col
A "character" string representing the name of the column of the SpiketypeFile containing the quantity of each control spiked in the Cy3 channel.
一个“字符”字符串，它表示列包含每个控制添加在Cy3标记通道的数量SpiketypeFile名称。


参数：cy5col
A "character" string representing the name of the column of the SpiketypeFile containing the quantity of each control spiked in the Cy5 channel.
一个“字符”字符串，它表示列包含每个控制添加在Cy5的通道数量SpiketypeFile名称。


参数：id
A "character" string describing which column of the MEEBO annotation should be used to retrieve replicated oligos, e.g. "SeqID".
一个“字符”字符串描述应使用Meebo的注解列检索复制寡核苷酸，例如： “SeqID”。


参数：namecol
A "character" string describing which column of the SpiketypeFile should be used in the legend.
一个“字”的SpiketypeFile栏应使用传说中的字符串描述。


参数：annot
A "character" string describing which R object should be used to look-up probes annotations. By default, it is set to MEEBOset.
一个“字符”字符串描述应该使用R对象看探针注释。默认情况下，它被设置为MEEBOset。


参数：bgMethod
Character string specifying which background correction method to use. See ?backgroundCorrect in package limma for more details.
字符串指定使用背景校正方法。看到了什么？更多细节在包limma backgroundCorrect。


参数：normMethod
Character string specifying which normalization method should be used. See ?normalizeWithinArrays in package limma for more details.
字符串指定应使用的规范化方法。有关详细信息，看到了什么？在包limma normalizeWithinArrays。


参数：diagnosticPlot
Logical. If 'TRUE', a quality diagnostic plot will be generated.
逻辑。如果“TRUE”，质量诊断图将会产生。


参数：output
Logical. If 'TRUE', normalized M values and A values corresponding to the input GenePix files and additionnal quality measures are printed to a file.
逻辑。如果“TRUE”，GenePix的输入文件和additionnal质量的措施相应的标准化的M值和A值打印到一个文件。


参数：resdir
A "character" string representing the directory where the results will be saved. By default, this is set to the current working directory (".").  
一个“字符”字符串表示的结果将被保存的目录。默认情况下，这是设置为当前工作目录（“。”）。


参数：dev
A "character" string naming the graphics device. This will take arguments "png", "jpeg" and "ps" only. By default, dev is set to "png".
一个“字符”字符串命名的图形设备。这将带参数的“PNG”，“JPEG”和“PS”只。默认情况下，开发设置“PNG”。


参数：organism
A "character" string naming the organism genome printed on the array, either "Mm" or "Hs". By default, organism is set to "Mm". It is used to retrieve the corresponding Oligo set annotations.
一个“字符”字符串命名的生物体的基因组阵列上，无论是“MM”或“HS”。默认情况下，机体被设置为“MM”。它是用来检索相应的寡集注释。


参数：DEBUG
If 'TRUE', debug statements are printed.
如果“TRUE”，打印调试语句。


参数：...
Additional arguments
额外的参数


Details

详情----------Details----------

meeboQuality returns 3 types of quality control plots, specifically designed for the various controls offered by the MEEBO set. To assess the global performance of an hybridization, users can generate a diagnostic plot summarizing several graphs and statictics by setting'diagnosticPlot=TRUE'. Then, the performance of the MEEBO set can beanalyzed by looking specifically at the mismatch and the tiling controls ('meeboSetQC=TRUE').
meeboQuality返回3种类型的质量控制图，专门为在Meebo集所提供的各种控件设计。为了评估全球的杂交性能，用户可以生成几个图表和settingdiagnosticPlot = TRUEstatictics诊断图总结。然后，Meebo的一套性能，可以beanalyzed专门寻找不匹配和平铺控件（meeboSetQC = TRUE“）。

Finally, we are also providing several exploratory tools to assess the performance of the doping-controls ('DOPING=TRUE');these plots should be used only if a spike-in mixture was added to the hybridization solution.
最后，我们还提供了一些探索性的工具，以评估的兴奋剂控制（“兴奋剂= TRUE”）的表现;只有当穗的混合物加入到杂交液应使用这些图。


值----------Value----------

meeboquality will produce several graphs, saved in an image file format. Please refer to the HTML description for more details. The function will also return the MAList object describing your tested slides.
meeboquality会产生几个图形，图像文件格式保存。更多详细信息，请参阅HTML描述。该函数也将返回描述你的测试的幻灯片的MAList对象。


作者（S）----------Author(s)----------


Agnes Paquet



参见----------See Also----------

meeboQualityPlots, gpQuality
meeboQualityPlots，gpQuality


举例----------Examples----------


if (interactive())
{
require(MEEBOdata)
datadir <- system.file("Meebo", package="MEEBOdata")
MA <- meeboQuality(fnames="RDI108_n.gpr",path=datadir,SpikeTypeFile="StanfordDCV1.7complete.txt",cy5col="CY5.ng._MjDC_V1.7",cy3col="CY3.ng._MjDC_V1.7",diagnosticPlot=TRUE,
DOPING=TRUE, meeboSetQC=TRUE, namecol="Name", resdir="MeeboQC", DEBUG=TRUE)
}

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。
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