read.mir(LVSmiRNA)
read.mir()所属R语言包：LVSmiRNA
Read in miRNA Data from Agilent Feature Extractiion Output Files
miRNA的数据读取安捷伦功能Extractiion的输出文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Reads intensitity data from a set of one-color microarray image analysis output files.
intensitity数据读取一套色芯片图像分析输出文件。
用法----------Usage----------
read.mir(files = NULL, path = NULL, ext = NULL, annotation=NULL,names = NULL, columns = list(E="gMedianSignal"),
other.columns = NULL, read.bg = TRUE,wt.fun = NULL, verbose = TRUE, sep = "\t", quote = "",
remove.ctrl=TRUE, ...)
参数----------Arguments----------
参数：files
data frame with column FileName giving the names of the files read, with column Sample giving the names of the samples.
与列的数据框FileName列，阅读文件的名称Sample给样品的名称。
参数：path
character string giving the directory containing the files. The default is the current working directory.
字符串，包含文件的目录。默认为当前工作目录。
参数：ext
character string giving optional extension to be added to each file name
被添加到每个文件名字符串，可选的扩展
参数：annotation
character vector of names of columns containing annotation information about the probes
特征向量包含有关探针的注释信息的列名
参数：names
character vector of names to be associated with each array as column name. Defaults to removeExt(files).
名称的字符向量与每个列名的数组。 removeExt(files)默认。
参数：columns
character vector of names of the required columns.
特征向量所需的列的名称。
参数：other.columns
character vector of names of additional required columns to be read.
额外所需的列名的字符向量被读取。
参数：read.bg
logical, TRUE to indicate background corrected values are read.
逻辑，TRUE表明背景修正值读取。
参数：wt.fun
function to calculate spot quality weights
函数来计算现场质量权重
参数：verbose
logical, TRUE to report each time a file is read
逻辑，TRUE报告每一个文件读取时间
参数：sep
the field separator character. Values on each line of the file are separated by this character.
字段分隔符。文件的每一行的值是通过这个角色分离。
参数：quote
character string of characters to be treated as quote marks
被视为引号字符字符串
参数：remove.ctrl
logical, if TRUE control probes will not be read
逻辑，如果TRUE控制探针将不会被读取
参数：...
any other arguments are passed to read.table
任何其他参数传递read.table的
Details
详情----------Details----------
This is the main data input function for the LVSmiRNA package for one-color microRNA data. It extracts the green channel intensities from a series of files, produced by Agilent Feature Extractiion software, and assembles them into the components of one list. Data from some other image analysis programs can be read if the appropriate column names containing the intensities are specified using the columns argument. (This will work if the column names are unique and if there are no incomplete rows in the file after the last line of data. Header lines are ok, if appropriately skipped.)
这是主要的数据输入功能LVSmiRNA色的microRNA数据包。它提取了一系列文件，由安捷伦特征Extractiion软件绿色通道强度，并把它们组合成一个列表组件。从一些其他的图像分析程序可以读取数据，如果使用columns参数指定相应的列名包含强度。 （这将工作，如果列名是独一无二的，如果有不完整的文件中没有行后的数据的最后一行。标题行是确定的，如果适当地跳过。）
The argument files should be a matrix with two columns at least. One column should contain the names of the samples and the other column should contain names of files containing intensity data.
参数files应该是一个至少两列的矩阵。一列应包含样品的名称，并应包含其他列包含强度数据的文件的名称。
The argument other.columns allows arbitrary columns of the image analysis output files to be reserved in the data object. These become matrices in the 'other' component.
参数other.columns允许被保留在数据对象的图像分析输出文件中的任意列。这些成为“其他”组件中的矩阵。
值----------Value----------
An Elist object.
一个Elist对象。
参数：G
matrix containing the intensities for each array with probes as rows and arrays as columns.
矩阵包含行和列的阵列探针为每个阵列的强度。
参数：Gb
matrix containing the background intensities for each array with probes as rows and arrays as columns.
矩阵包含行和列的阵列探针为每个阵列的背景强度。
参数：targets
data frame with column FileName giving the names of the files read, with column Sample giving the names of the samplse.
数据柱框架FileName给的文件名读取列，Sample的的samplse给予的名称。
参数：genes
data frame containing annotation information about the probes, for examples miRNA names and IDs and positions on the array.
数据框的例子包含有关探针的注释信息，miRNA的阵列上的名称和ID和位置。
参数：source
character string giving the image analysis program name.
给图像分析程序名称的字符串。
参数：preprocessing
list with components Background, Normalization, is.log, Summarization indicate which pre-processing step has beendone.
与组件列表Background，Normalization，is.log，Summarization表明前处理步骤beendone。
注意----------Note----------
All image analysis files being read are assumed to contain data for the same genelist in the same order. No checking is done to confirm that this is true. Probe annotation information is read from one of the files only.
所有图像分析正在阅读的文件被认为包含在同一顺序相同genelist的数据。做任何检查，以确认这是真的。从一个文件只读取探针注释信息。
作者（S）----------Author(s)----------
Stefano Calza <stefano.calza@biostatistics.it>, Suo Chen and Yudi Pawitan.
参见----------See Also----------
read.mir is based on "read.table" in the base package and modified from "read.maimages" in the limma
read.mir是基于"read.table"在基础包和修改从"read.maimages"limma了
举例----------Examples----------
# Read all intensity files from current working directory[阅读强度从当前工作目录的所有文件]
## Not run: [＃无法运行：]
dir.files <- system.file("extdata", package="LVSmiRNA")
taqman.data <- read.table(file.path(dir.files,"Comparison_Array.txt"),header=TRUE,as.is=TRUE)
MIR <- read.mir(taqman.data)
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 23:53:46
