readCtData(HTqPCR)
readCtData()所属R语言包：HTqPCR
Reading Ct values from qPCR experiments data into a qPCRset
读成qPCRset的qPCR实验数据的CT值
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function will read tab separated text files with Ct values and feature meta-data from high-throughput qPCR experiments into a qPCRset containing all the relevant information.
此功能将阅读与Ct值和高通量的qPCR实验功能元数据包含所有相关信息qPCRset制表符分隔的文本文件。
用法----------Usage----------
readCtData(files, path = NULL, n.features = 384, flag = 4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, SDS = FALSE, n.data = 1, samples, na.value = 40, ...)
参数----------Arguments----------
参数：files
character vector witht he names of the files to be read.
字符向量witht的他要读取的文件的名称。
参数：path
character string with the path to the folder containing the data files.
字符串包含数据文件的文件夹的路径。
参数：n.features
integer, number of features present in each file.
整数，多项功能呈现在每个文件中。
参数：flag
integer indicating the number of column containing information about the flags. See Details.
整数，指示列包含有关标志的信息。查看详细信息。
参数：feature
integer indicating the number of column containing information about the individual features (typically gene names).
整数，指示列包含有关个人特征的信息（通常是基因名称）的数量。
参数：type
integer indicating the number of column containing information about the type of each feature. See Details.
整数，指示列包含关于每个功能的类型的信息的数量。查看详细信息。
参数：position
integer indicating the number of column containing information about the position of features on the card. See Details.
整数，指示列包含的功能卡上的位置信息。查看详细信息。
参数：Ct
integer indicating the number of column containing information about the Ct values.
整数，表示Ct值的列，其中包含有关信息的数量。
参数：header
logical, does the file contain a header row or not.
逻辑，该文件不包含标题行或没有。
参数：SDS
logical, is the data in the output format from Sequence Detection Systems (SDS) Software. See Details.
逻辑，是在从序列检测系统（SDS）软件的输出格式的数据。查看详细信息。
参数：n.data
integer vector, same length as files. Indicates the number of samples that are present in each file. For each file n.data*n.features lines will be read.
整数向量，相同长度为files。表示在每个文件中的样本数。对于每个文件n.data * n.features线将被读取。
参数：samples
character vector with names for each sample. Per default the file names are used.
每个样本的名称与特征向量。每个默认的文件名。
参数：na.value
integer, a Ct value that will be assigned to all undetermined/NA wells.
整数，Ct值将分配给所有未定/ N井。
参数：...
any other arguments are passed to read.table.
任何其他的参数被传递到read.table。
Details
详情----------Details----------
This is the main data input function for the HTqPCR package for analysing qPCR data. It extracts the threshold cycle, Ct value, of each well on the card, as well as information about the quality (e.g.~passed/failed) of the wells. The function is tuned for data from TaqMan Low Density Array cards, but can be used for any kind of qPCR data.
这是HTqPCR qPCR数据分析软件包的主要数据输入功能。它提取的循环阈值，以及每个卡上的Ct值，以及有关质量的信息（例如~通过/失败）的水井。该功能是调整的TaqMan低密度阵列卡的数据，但可以使用任何一种qPCR数据。
featureNames, featureType and featurePos will be extracted from the first file. If flag, type or position er set to NULL, this means that this information is not available in the file. flag will then be set to "Passed", type to "Target" and position to "feature1", "feature2", ... etc until the end of the file. Especially position might not be available in case the data does not come from a card format, but it is required in subsequent functions in order to disambiguate between features in case some features are present multiple times.
featureNames，featureType和featurePos将提取从第一个文件。如果flag，type或position呃设置为NULL，这意味着，这个信息是在文件中没有提供。 flag然后将被设置为“合格”，type“目标”和position“特性1”，“1特性”，...等，直到文件结束。尤其是position可能不会提供数据的情况下并不来自卡格式，但它在随后的功能要求，以特征之间的歧义的情况下，有些功能是目前多次。
If the data was analysed using SDS Software it may contain a variable length header specifying parameters for files that were analysed at the same time. If SDS=TRUE then readCtData will scan through the first 100 lines of each file, and skip all lines until (and including) the line beginning with "#", which is the header. The end of the file might also contain some plate ID information, but only the number of lines specified in n.features will be read.
如果对数据进行分析，使用SDS软件，它可能包含一个可变长度的头指定参数，同时分析的文件。如果SDS=TRUE然后readCtData会通过每个文件的第100行扫描，跳过所有之前线（含）的行的开头以“＃”，这是头。文件末尾还可能包含一些板块的ID信息，但只有在n.features指定的行数将读取。
值----------Value----------
A "qPCRset" object.
一个"qPCRset"对象。
警告----------Warnings----------
The files are all assumed to belong to the same design, i.e.~have the same features (genes) in them and in identical order.
假设文件都属于相同的设计，即有相同的功能，他们在同一顺序（基因）。
作者（S）----------Author(s)----------
Heidi Dvinge
参见----------See Also----------
read.delim for further information about reading in data, and "qPCRset" for a definition of the resulting object.
read.delim读取数据，"qPCRset"生成的对象的定义的进一步信息。
举例----------Examples----------
# Locate example data and create qPCRset object[找到示例数据，和创建qPCRset对象]
exPath <- system.file("exData", package="HTqPCR")
exFiles <- read.delim(file.path(exPath, "files.txt"))
raw <- readCtData(files=exFiles$File, path=exPath)
# Example of adding missing information (random data in this case)[例如添加丢失的信息（在这种情况下，随机数据）]
featureClass(raw) <- factor(rep(c("A", "B", "C"), each=384/3))
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 21:52:25
