constructInf(crlmm)
constructInf()所属R语言包：crlmm
Instantiate an object of class CNSet for the Infinium platforms.
Infinium平台CNSet类实例化一个对象。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Instantiates an object of class CNSet for the Infinium platforms. Elements of assayData and batchStatistics will be ff objects. See details.
实例化一个对象类CNSet Infinium平台。 assayData和batchStatistics会ff对象的元素。查看详情。
用法----------Usage----------
constructInf(sampleSheet = NULL, arrayNames = NULL, path = ".", arrayInfoColNames = list(barcode = "SentrixBarcode_A", position = "SentrixPosition_A"), highDensity = FALSE, sep = "_", fileExt = list(green = "Grn.idat", red = "Red.idat"), cdfName, verbose = FALSE, batch, saveDate = TRUE)
参数----------Arguments----------
参数：sampleSheet
data.frame containing Illumina sample sheet information (for required columns, refer to BeadStudio Genotyping guide - Appendix A).
data.frame含有Illumina的样品表信息（所需的列，请参阅BeadStudio基因分型指南 - 附录A）。
参数：arrayNames
character vector containing names of arrays to be read in. If NULL, all arrays that can be found in the specified working directory will be read in.
包含数组的名字被读入。如果NULL，可以在指定的工作目录中找到的所有阵列将读入的字符向量
参数：path
character string specifying the location of files to be read by the function
字符串功能读取指定文件的位置
参数：arrayInfoColNames
(used when sampleSheet is specified) list containing elements 'barcode' which indicates column names in the sampleSheet which contains the arrayNumber/barcode number and 'position' which indicates the strip number. In older style sample sheets, this information is combined (usually in a column named 'SentrixPosition') and this should be specified as list(barcode=NULL, position="SentrixPosition")
（用时sampleSheet指定）包含元素的条码“表示sampleSheet其中包含的arrayNumber /条码号和”立场“表示条数列名的列表。在旧式的样品表，此信息相结合（通常在一列名为“SentrixPosition”），这应作为list(barcode=NULL, position="SentrixPosition")指定
参数：highDensity
logical (used when sampleSheet is specified). If TRUE, array extensions '\_A', '\_B' in sampleSheet are replaced with 'R01C01', 'R01C02' etc.
逻辑（当sampleSheet指定使用）。如果TRUE，阵列扩展\ _A，\ _B“在sampleSheet取代R01C01，R01C02”等。
参数：sep
character string specifying separator used in .idat file names.
字符串指定分隔符使用。IDAT文件名。
参数：fileExt
list containing elements 'Green' and 'Red' which specify the .idat file extension for the Cy3 and Cy5 channels.
列表，其中包含元素的绿色和红指定文件扩展名。IDAT Cy3和Cy5通道。
参数：cdfName
annotation package (see also validCdfNames)
注释包（又见validCdfNames）
参数：verbose
'logical.' Whether to print descriptive messages during processing.
“逻辑。”是否打印在加工过程中的描述信息。
参数：batch
batch variable. See details.
批处理中的变量。查看详情。
参数：saveDate
'logical'. Should the dates from each .idat be saved with sample information?
“逻辑”。应该从每个。IDAT日期与样品信息被保存？
Details
详情----------Details----------
This function initializes a container for storing the normalized intensities for the A and B alleles at polymorphic loci and the normalized intensities for the 'A' allele at nonpolymorphic loci. CRLMM genotype calls and confidence scores are also stored in the assayData. This function does not do any preprocessing or genotyping – it only creates an object of the appropriate size. The initialized values will all be 'NA'.
这个函数初始化一个容器存放在多态位点和归强度为“A”在nonpolymorphic位点的等位基因A和B等位基因的归强度。 CRLMM的基因型分型和信心分数也存储在assayData。此功能没有做任何预处理或基因分型 - 只创建一个适当大小的对象。的初始值都将是“不适用”。
The ff package provides infrastructure for accessing and writing data to disk instead of keeping data in memory. Each element of the assayData and batchStatistics slot are ff objects. ff objects in the R workspace contain pointers to several files with the '.ff' extension on disk. The location of where the data is stored on disk can be specified by use of the ldPath function. Users should not move or rename this directory. If only output files are stored in ldPath, one can either remove the entire directory prior to rerunning the analysis or all of the '.ff' files. Otherwise, one would accumulate a large number of '.ff' files on disk that are no longer in use.
FF包提供了用于访问和写入数据到磁盘上，而不是保存在内存中的数据的基础设施。每个元素assayData和batchStatistics插槽是FF的对象。在R工作区的FF对象包含FF扩展磁盘上的几个文件的指针。数据存储在磁盘上的位置，可以指定由ldPath函数的使用。用户不应移动或重命名此目录。如果只输出文件存储在ldPath，一个可以删除整个目录前重新运行分析或FF所有文件。否则，一会积累了大量的FF的磁盘上的文件，不再使用。
We have adopted the ff package in order to reduce crlmm's memory footprint. The memory usage can be fine-tuned by the utilities ocSamples and ocProbesets provided in the oligoClasses package. In most instances, the user-level interface will be no different than accessing data from ordinary matrices in R. However, the differences in the underlying representation can become more noticeable for very large datasets in which the I/O for accessing data from the disk can be substantial.
我们已采取了ff包，以减少crlmm的内存占用。内存使用情况，可以通过公用事业微调ocSamples和ocProbesetsoligoClasses包中提供。在大多数情况下，不会比访问从普通矩阵R中的数据，但不同的用户界面，可以在底层表示差异非常大的数据集变得越来越明显，在从磁盘访问数据的I / O可以十分重大。
值----------Value----------
A CNSet object
一个CNSet对象
作者（S）----------Author(s)----------
R. Scharpf
参见----------See Also----------
ldPath, ocSamples, ocProbesets, CNSet-class, preprocessInf, genotypeInf
ldPath，ocSamples，ocProbesets，CNSet-class，preprocessInf，genotypeInf
举例----------Examples----------
## See the illumina_copynumber.Rnw vignette in inst/scripts of the[＃在本月illumina_copynumber.Rnw暗角/脚本]
## source package for an example[＃源码包的例子]
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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发表于 2012-2-25 16:02:14
