read.rg(CALIB)
read.rg()所属R语言包：CALIB
Read RGList\_CALIB from Image Analysis Output Files
从图像分析输出文件阅读RGList \ _CALIB
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Reads an RGList\_CALIB from a series of microarray image analysis output files
读取系列芯片图像分析输出文件RGList \ _CALIB
用法----------Usage----------
read.rg(files = NULL, source = "generic", path = NULL, ext = NULL,
names = NULL, columns = NULL, other.columns = NULL,
annotation = NULL,wt.fun = NULL, verbose = TRUE, sep = "\t",
quote = NULL, DEBUG = FALSE, ...)
参数----------Arguments----------
参数：files
character vector giving the names of the files containing image analysis output or, for Imagene data, a character matrix of names of files. If omitted, then all files with extension ext in the specified directory will be read in alphabetical order.
特征向量包含图像分析输出文件的名称或Imagene数据，文件名的字符点阵。如果省略，则所有副档名为ext在指定的目录中，将在按字母顺序阅读。
参数：source
character string specifying the image analysis program which produced the output files. Choices are "generic", "agilent", "arrayvision", "bluefuse", "genepix", "genepix.custom", "genepix.median",<br> "imagene", "quantarray", "scanarrayexpress", "smd.old", "smd",<br> "spot" or "spot.close.open".
字符串指定的图像分析程序产生的输出文件。选择是"generic"，"agilent"，"arrayvision"，"bluefuse"，"genepix"，"genepix.custom"，"genepix.median"参考<X >，"imagene"，"quantarray"，"scanarrayexpress"，"smd.old"参考"smd"或"spot"。
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：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
list with fields R, G, Rb, Gb, RArea and GArea giving the column names to be used for red foreground, green foreground, red background, green background, red area and green area respectively. Or, in the case of Imagene data, a list with fields f and b. This argument is optional if source is specified, otherwise it is required.
与字段列表R，G，Rb，Gb，RArea和GArea列名称用红色前景，绿色前景，红色背景，绿色背景，红色区域和绿色区域分别。或者，在Imagene数据的情况下，列表字段f和b。 source如果指定此参数是可选的，否则它是必需的。
参数：other.columns
character vector of names of other columns to be read containing spot-specific information
其他列名的字符向量含特定点信息读取
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：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
字段分隔符
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：DEBUG
a logical value, if TRUE, a series of echo statements will be printed for each file. Details on the file, skip, and selected columns in a colClasses format for read.table will be displayed.
一个逻辑值，如果TRUE，一系列echo语句将打印每个文件。将显示文件，请跳过细节，并选定列read.table在colClasses格式。
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 CALIB package. It has the similar usage as the read.maimages function in limma package. The output of the function is an RGList_CALIB object. However,there are two more fields - $RArea and $GArea than RGList object in limma package. These two fields contain spot area of each color. More details see read.maimages in limma package.
这是CALIB包的主要数据输入功能。它有类似的用法，作为read.maimages功能limma包。该函数的输出是一个RGList_CALIB对象。然而，有两个字段 - $RArea和$GArea比RGList的limma包对象。这两个领域包含当场每种颜色的区域。更多细节见read.maimages的limma在包。
值----------Value----------
An RGList_CALIB object containing the components
RGList_CALIB对象，其中包含的组件
参数：R
matrix containing the red channel foreground intensities for each spot for each array.
当场为每个阵列的每个矩阵包含红色通道前景强度。
参数：G
matrix containing the green channel foreground intensities for each spot for each array.
当场为每个阵列的每个矩阵包含绿色通道前景强度。
参数：Rb
matrix containing the red channel background intensities for each spot for each array.
当场为每个阵列的每个矩阵包含红色通道的背景强度。
参数：Gb
matrix containing the green channel background intensities for each spot for each array.
当场为每个阵列的每个矩阵包含绿色通道背景强度。
参数：RArea
matrix containing the red spot area for each spot for each array.
矩阵包含每个阵列的每个点的红色斑点面积。
参数：GArea
matrix containing the green spot area for each spot for each array.
矩阵包含每个阵列的每个点的绿斑面积。
参数：weights
spot quality weights, if wt.fun is given
现场质量权重，如果wt.fun给出
参数：other
list containing matrices corresponding to other.columns if given
列表，其中包含矩阵对应other.columns如果给
参数：genes
data frame containing annotation information about the probes, for example gene names and IDs and spatial positions on the array, currently set only if source is "agilent", "genepix" or source="imagene" or if the annotation argument is set
数据框包含有关探针注释信息，例如基因的名称和ID和阵列上的空间位置，目前只有source是"agilent"，"genepix"或source="imagene"或如果annotation参数设置
参数：targets
data frame with column FileName giving the names of the files read
数据柱框架FileName给的文件名读取
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：printer
list of class PrintLayout, currently set only if source="imagene"
类列表PrintLayout，目前只有source="imagene"
作者（S）----------Author(s)----------
Hui Zhao
参考文献----------References----------
<h3>See Also</h3>
举例----------Examples----------
# Read all .gpr files from current working directory.[阅读所有从当前工作目录。GPR文件。]
# files <- dir(pattern="*\.gpr$")[文件< - DIR =“* \ GPR $（模式”）]
# RG <- read.rg(files,"genepix")[的RG < - read.rg人（文件，“genepix）]
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。
|
发表于 2012-2-25 14:01:37
