readPlateList(cellHTS2)
readPlateList()所属R语言包：cellHTS2
Read a collection of plate reader data files
阅读酶标仪数据文件的集合
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Reads a collection of plate reader data files into a cellHTS object. The names of the files, plus additional information (plate number, repeat number, assay/treatment/condition) is expected to be stored in a tab-delimited table specified by the argument filename. Alternatively, the data can be provided directly from non file-based sources, e.g. a data base (see details).
读入一个cellHTS对象酶标仪数据文件的集合。预计将在由参数filename指定制表符分隔的表存储的文件的名称，再加上额外的信息（车牌号码，重复号码，检测/治疗/条件）。此外，数据可以直接从非基于文件的来源，如提供一个数据库（见详情）。
用法----------Usage----------
readPlateList(filename, path=NA, name="anonymous", importFun,
dec=".", verbose=interactive(), ...)
参数----------Arguments----------
参数：filename
the name of the plate list file (see details). This argument is just passed on to the read.table function, so any of the valid argument types for the file argument of read.table are valid here, too. Alternatively, a user-defined function which is supposed to create a table-like R object of the plate list. Additional arguments to readPlateList in ... will be passed on to this function.
板列表文件的名称（见详情）。这种说法只是通过read.table函数，所以任何file read.table参数的有效参数类型是有效的，在这里，太。另外，用户定义的功能，这是为了创建一个表，如R板块列表的对象。额外的参数readPlateList...将被传递给这个函数。
参数：path
a character of length 1 indicating the path in which to find the plate reader files. If the importFun argument is supplied, the value of path will not be automatically prepended to the file names. This has to be explicitely dealt with in the importFun function. See details.
一个长度为1的字符显示在其中找到酶标仪文件路径。如果importFun参数提供值path将不会被自动追加到文件名。这importFun函数可以明确地处理。查看详情。
参数：name
a character of length 1 with the experiment name.
1，实验名称长度的字符。
参数：importFun
a function to read the data files. The default function works for a certain file format, such as that of the example files provided with this package. If your plate reader software produces files with a different format or if you want to import data from a non file-based source, the import function needs to be adapted. See details and examples.
一个函数来读取数据文件。默认功能为一个特定的文件格式，这个包提供的示例文件，如。如果您的酶标仪软件产生不同格式的文件，或者如果你想从一个非基于文件的源导入数据，导入功能，需要适应。细节和例子。
参数：dec
Optional argument that is passed to importFun, and can be used to accommodate for data files that use characters different from . to represent the decimal point (e.g., the comma ,).
可选参数，传递到importFun的，可以用来容纳数据文件，使用不同的字符.代表小数点（例如，逗号,）。
参数：verbose
a logical value, if TRUE, the function reports some of its intermediate progress.
一个逻辑值，如果属实，功能及其中间体的进展报告。
参数：...
additional arguments that are being passed on to filename if it is a function.
正在传递给filename额外的参数，如果它是一个函数。
Details
详情----------Details----------
The plate list is expected to be a tab-delimited file with at least three columns named Filename, Plate, and Replicate. The contents of the columns Plate and Replicate are expected to be integers. Filename should be a vector of file names of the respective raw data files. If the path argument is supplied and importFun is missing, its value will automatically be prepended to the file names. The optional Batch column can be used to supply batch information for an experiment, e.g., when a reagent has been changed or the experiment has been run over several days.
预计该板块列表是一个制表符分隔的文件名为Filename，Plate，Replicate至少有三个列。列的内容Plate和Replicate预计将整数。 Filename各自的原始数据文件的文件名应该是一个向量。如果path参数提供importFun丢失，其价值将被自动追加到文件名。可选Batch列可以被用来提供一个实验批次信息，例如，当试剂已被更改或实验已运行了几天。
Further columns are allowed, and can be used to denote, for example, different variants of the assay, treatments, incubation times, conditions, etc.
进一步列是允许的，可以用来表示，例如，不同变种的检测，治疗，孵化时间，条件等。
Alternatively, the value of filename can be a user-defined function which creates a data.frame similar to the one described before. This is for instance useful if the plate list information is directly imported from a data base. In order to allow for non-elementary data types, the output of the function can also be a named list, where each element has to be a vector of equal length. The aforementioned type restrictions still apply. The function will be called with all additional ... arguments, which allows to pass in additional information like experiment identifiers or data base queries.
另外，filename价值可以是一个用户定义的函数创建一个data.frame类似前一个。这是有用的实例，如果直接从数据的基础上进口板列表信息。为了让非基本数据类型，函数的输出也可以是一个命名的列表，其中每个元素是一个长度相等的向量。上述类型的限制仍然适用。所有额外的函数将被调用...参数，它允许通过的其他信息，如实验标识符或数据的基础上查询。
importFun can be used to define a custom function to import data files. The importFun function should accept as its first argument names from the Filename column of the plate list (which in principle do not need to be individual files, they could also be handles for database entries, queries, or pointers into relevants parts of a file). As it second argument, the function should accept the value of the path argument, and the user needs to explicitely prepend this to the file names if needed. It should return a list with two components:
importFun可用于自定义一个函数来导入数据文件。 importFun函数应接受作为其第一个参数Filename列板的名单（这在原则上并不需要单个文件名，他们也可能是数据库条目，查询，或把手指针到一个文件相关者的部分）。作为它的第二个参数，函数应该接受path参数值，用户需要明确地在前面加上这个文件名，如果需要的话。两部分组成，它应该返回一个列表：
The first component should be a data.frame with the following columns
第一部分应该是一个与下面的列data.frame
well, a character vector with the well identifier in the plate.
well，以及在板标识与特征向量。
val, the intensity values measured in that well.
val，强度，以及测量值。
and with as many rows as there are wells in the plate.
与许多行板有井。
The second component should be a character vector containing a copy of the imported input data file (such as the output of readLines). It should be suitable to be used as input for writeLines, since it will be used to reproduce the intensity files that are linked in the HTML quality reports generated by writeReport.
第二部分应该是一个特征向量，包含进口的输入数据文件副本（如输出readLines）。它应该是适合用作为writeLines的输入，因为它会被用来重现强度链接文件是在质量writeReport生成的HTML报告。
For example, to import plate data files from EnVision plate reader, set importFun=getEnVisionRawData or importFun=getEnvisionCrosstalkCorrectedData. See function getEnVisionRawData.
例如，进口板的数据文件，从设想酶标仪，设置importFun=getEnVisionRawData或importFun=getEnvisionCrosstalkCorrectedData。见功能getEnVisionRawData。
Direct data base import without the need for any flat files at all could for instance be archived by:
直接的数据，而不需要在任何平面文件的基础进口，例如存档：
Providing a user-defined function as the filename argument and an experiment identifier as an additional ... argument. The function would have to query the data base for the plate information using this identifier and return a table as described above, where the Filename column contains identifiers needed to fetch the respective raw data for a single plate in a subsequent query. Alternatively, this could be a data base handle, or the query itself.
作为filename参数和实验标识符作为一个额外的提供用户定义的函数...参数。该功能将有板使用此标识的信息查询数据的基础上，并返回作为以上所述的表，其中Filename列包含需要取各自的原始数据，在随后的查询单盘的标识符。另外，这可能是一个数据库句柄，或查询本身。
Providing a second user-defined function as the importFun argument, which takes the value of the Filename column for a single plate and retrieves the respective raw data from the data base.
提供作为importFun的说法，这需要一个单一的板Filename列的值和检索数据的基础上，从各自的原始数据的第二个用户定义的函数。
值----------Value----------
An object of class cellHTS, which extends the class NChannelSet.
一个对象类cellHTS，延伸类的NChannelSet。
After calling this function, the content of the following slots is as follows:
调用这个函数后，下面的插槽内容如下：
参数：assayData
an object of class AssayData containing the imported measurement data. Each matrix represents a single channel, and each run corresponds to a column. Thus, the total number of rows in each matrix corresponds to the product between the number of wells per plate and the number of assay plates.
一个类的对象AssayData包含进口的测量数据。每个矩阵代表一个通道，每次运行对应的一列。因此，每个矩阵中的行的总数相当于每盘的井数和数量的检测板之间的产品。
参数：phenoData
information about the runs, inferred from the plateList file: which replicate, which variant of the assay, treatment, incubation times etc.
推断plateList文件的运行，复制，变异的检测，治疗，孵化时间等信息
参数：featureData
the information about the plate and well identifiers for each plate measurement are stored in columns plate and well of this slot.
在列中存储的有关信息板，每块板测量以及标识符plate和well这个槽。
参数：plateList
a data.frame containing what was read from input file x, plus a column status of type character: it contains the string "OK" if the data import appeared to have gone well, and the respective error or warning message otherwise.
数据框，其中包含从读取输入文件x，加列status型性格：它包含字符串“OK”，如果出现数据导入顺利，各自否则错误或警告消息。
参数：intensityFiles
a list, where each component contains a copy of the imported input data files. Its length corresponds to the number of rows of plateList.
一个列表，其中每个组件包含了进口输入数据文件副本。它的长度相当于plateList行的数目。
作者（S）----------Author(s)----------
W. Huber <a href="mailto:huber@ebi.ac.uk">huber@ebi.ac.uk</a>, Ligia Bras <a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>,
Florian Hahne <a href="mailto:florian.hahne@novartis.com">florian.hahne@novartis.com</a>
参考文献----------References----------
screens, Genome Biology 7, R66.
参见----------See Also----------
To read input files obtained in a HTanalyser plate reader, see readHTAnalystData. To build a cellHTS2 object from a data frame, see buildCellHTS2.
要读取输入文件获得在HTanalyser酶标仪，看到readHTAnalystData。 1 cellHTS2对象来构建一个数据框，看到buildCellHTS2。
举例----------Examples----------
datadir <- system.file("KcViabSmall", package = "cellHTS2")
x <- readPlateList("Platelist.txt", "KcViabSmall", path=datadir)
## To read data files obtained from an EnVision plate reader:[＃读取与设想酶标仪获得的数据文件：]
datadir <- system.file("EnVisionExample", package = "cellHTS2")
x <- readPlateList("platelist.txt", name="EnVisionEx",
importFun=getEnVisionRawData, path=datadir)
## to get the cross talk corrected data:[＃相声修正后的数据：]
y <- readPlateList("platelist.txt", name="EnVisionEx",
importFun=getEnVisionCrosstalkCorrectedData, path=datadir)
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。
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发表于 2012-2-25 14:17:58
