read.maimages(limma)
read.maimages()所属R语言包：limma
Read RGList or EListRaw from Image Analysis Output Files
从图像分析输出文件或阅读RGList EListRaw
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Reads an RGList from a set of two-color microarray image analysis output files, or an EListRaw from a set of one-color files.
读取RGList从一组两色的生物芯片图像分析输出文件，或从一组彩色文件EListRaw。
用法----------Usage----------
read.maimages(files=NULL, source="generic", path=NULL, ext=NULL, names=NULL,
columns=NULL, other.columns=NULL, annotation=NULL, green.only=FALSE,
wt.fun=NULL, verbose=TRUE, sep="\t", quote=NULL, ...)
read.imagene(files, path=NULL, ext=NULL, names=NULL, columns=NULL, other.columns=NULL,
wt.fun=NULL, verbose=TRUE, sep="\t", quote="\"", ...)
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", "agilent.median", "arrayvision", "arrayvision.ARM", "arrayvision.MTM", "bluefuse", "genepix", "genepix.custom", "genepix.median", "imagene", "imagene9", "quantarray", "scanarrayexpress", "smd.old", "smd", "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"，"agilent.median"，"arrayvision"，"arrayvision.ARM"，"arrayvision.MTM"，"bluefuse"，"genepix" "genepix.custom"，"genepix.median"，"imagene"，"imagene9"，"quantarray"，"scanarrayexpress"，"smd.old"，"smd"，"spot"或"spot.close.open"。
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, or named character vector. For two color data, this should have fields R, G, Rb and Gb giving the column names to be used for red and green foreground and background or, in the case of Imagene data, a list with fields f and b. For single channel data, the fields are usually E and Eb. This argument is optional if source is specified, otherwise it is required.
列表，或指定的字符向量。两种颜色的数据，这应该有领域的R，G，Rb和Gb给为红色和绿色的前景和背景的列名，或在Imagene数据的情况下，列表字段f和b。对于单通道数据，字段通常是E和Eb。 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：green.only
logical, for use with source, should the green (Cy3) channel only be read, or are both red and green required?
逻辑，使用source，绿色通道（Cy3标记）只能读取，或者是红色和绿色的要求？
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：...
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 LIMMA package for two-color microarray data. It extracts the foreground and background intensities from a series of files, produced by an image analysis program, and assembles them into the components of one list. The image analysis programs Agilent Feature Extraction, ArrayVision, BlueFuse, GenePix, ImaGene, QuantArray (Version 3 or later), Stanford Microarray Database (SMD) and SPOT are supported explicitly. Data from some other image analysis programs can be read if the appropriate column names containing the foreground and background intensities are specified using the columns argument. (This will work if the column names are unique and if there are no rows in the file after the last line of data. Header lines are ok.)
这是主要的数据LIMMA包两色的微阵列数据的输入功能。它从一系列图像分析程序产生的文件，提取的前景和背景的强度，并把它们组合成一个列表组件。图像分析方案安捷伦特征提取，ArrayVision，BlueFuse，GenePix，ImaGene，QuantArray（3或更高版本），斯坦福芯片数据库（SMD）和SPOT的明确支持。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称中含有的前景和背景强度。 （这将工作，如果列名是独一无二的，如果有文件没有行后的数据的最后一行。标题行是确定的。）
SMD data should consist of raw data files from the database, in tab-delimited text form. There are two possible sets of column names depending on whether the data was entered into the database before or after September 2003. source="smd.old" indicates that column headings in use prior to September 2003 should be used. In the case of Agilent and GenePix, two possible foreground estimators are supported: source="genepix" uses the mean foreground estimates while source="genepix.median" uses median foreground estimates. Similarly for Agilent. GenePix 6.0 and later also supplies some custom background options, notably morphological background. If the GPR files have been written using a custom background, you may read it using source="genepix.custom". In the case of SPOT, two possible background estimators are supported: if source="spot.close.open" then background intensities are estimated from morph.close.open rather than morph.
贴片的数据应包括从数据库中的原始数据文件，制表符分隔的文本形式。进入到2003年9月之前或之后的数据库中的数据是否被列名的可能有两个套。 source="smd.old"表示在使用该列标题应使用至2003年9月之前。在安捷伦和GenePix的情况下，支持两种可能的前景估计：source="genepix"使用的平均前景的估计，而source="genepix.median"使用中位数前景的估计。同样，对于安捷伦。 GenePix 6.0和更高版本中还提供了一些自定义背景的选项，尤其是形态背景。如果GPR文件已被写入使用自定义的背景，你可以读它使用source="genepix.custom"。在了现场的情况下，两种可能的背景估计支持：如果source="spot.close.open"然后背景强度morph.close.open而不是morph估计。
Spot quality weights may be extracted from the image analysis files using a weight function wt.fun. wt.fun may be any user-supplied function which accepts a data.frame argument and returns a vector of non-negative weights. The columns of the data.frame are as in the image analysis output files. There is one restriction, which is that the column names should be refered to in full form in the weight function, i.e., do not rely on name expansion for partial matches when refering to the names of the columns. See QualityWeights for suggested weight functions.
现场质量权重，可以提取使用图像分析权函数wt.fun文件。 wt.fun可能是任何用户提供的函数，它接受一个数据框的参数，并返回一个非负权重向量。数据框列在图像分析输出文件。有一个限制，这是列名应参考中的权重函数的完整形式，即不依靠部分匹配的扩展名时参考列的名称。看到QualityWeights建议的体重职能。
For data from ImaGene versions 1 to 8 (source="imagene"), the argument files should be a matrix with two columns. The first column should contain the names of the files containing green channel (cy3) data and the second column should contain names of files containing red channel (cy5) data. If source="imagene" and files is a vector of even length instead of a matrix, then each consecutive pair of file names is assumed to correspond to the same array. The function read.imagene is called by read.maimages when source="imagene". It does not need to be called directly by users. For ImaGene 9 (source="imagene9"), files is a vector as for other image analysis programs.
为从1到8（source="imagene"），参数files应该具有两列的矩阵ImaGene版本的数据。第一列应该包含绿色通道（CY3）和第二列的数据应该包含含有红色通道（CY5）数据文件的名称包含文件的名称。如果source="imagene"和files是一个甚至长度，而不是一个矩阵向量，然后连续对每个文件名假设对应相同的阵列。功能read.imagene被称为read.maimages时source="imagene"。它并不需要，可以由用户直接调用。对于ImaGene 9（source="imagene9"）files是一个向量，为其他图像分析程序。
ArrayVision reports spot intensities in a number of different ways. read.maimages caters for ArrayVision's Artifact-removed (ARM) density values as "arrayvision.ARM" or for Median-based Trimmed Mean (MTM) density values as "arrayvision.MTM". ArrayVision users may find it useful to read the top two lines of their data file to check which version of density values they have.
ArrayVision报告在许多不同的方式当场强度。 read.maimages迎合ArrayVision的神器，删除“（ARM）"arrayvision.ARM"或"arrayvision.MTM"密度值中位数为基础的修剪平均值（MTM）的密度值。 ArrayVision用户可能会发现它有用读取其数据文件的前两个线，以检查他们有哪个版本的密度值。
The argument other.columns allows arbitrary columns of the image analysis output files to be preserved in the data object. These become matrices in the component other component. For ImaGene data, the other column headings with be prefixed with "R " or "G " as appropriate.
参数other.columns允许在保存数据对象的图像分析输出文件中的任意列。这些成为组件other组件矩阵。 ImaGene数据，其他列标题"R "或"G "适当的前缀。
值----------Value----------
For one-color data, an EListRaw object. For two-color data, an RGList object containing the components
对于一个色彩数据，EListRaw对象。对于两色数据，RGList对象包含的组件
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：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：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：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：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"
警告----------Warnings----------
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 the first file 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。探针注释信息读取只从第一个文件。
作者（S）----------Author(s)----------
Gordon Smyth, with speed improvements by Marcus Davy
参考文献----------References----------
参见----------See Also----------
read.maimages uses read.columns for efficient reading of text files. As far as possible, it is has similar behavior to read.table in the base package.
read.maimages使用read.columns高效阅读的文本文件。尽可能，它是有类似的行为read.table基本包。
An overview of LIMMA functions for reading data is given in 03.ReadingData.
在03.ReadingData一个读取数据LIMMA功能的概述。
举例----------Examples----------
# Read all .gpr files from current working directory[从当前的工作目录读取。GPR文件]
# and give weight 0.1 to spots with negative flags[重量0.1点与负的标志]
## Not run: files <- dir(pattern="*\\.gpr$")[＃无法运行：文件< - DIR =“* \ \ GPR $”（模式）]
RG <- read.maimages(files,"genepix",wt.fun=wtflags(0.1))
## End(Not run)[＃结束（不运行）]
# Read all .spot files from current working director and down-weight[阅读从当前工作主任和体重下降。当场文件]
# spots smaller or larger than 150 pixels[斑点较小或大于150像素]
## Not run: files <- dir(pattern="*\\.spot$")[＃无法运行：< - 目录文件（模式=“* \ \现货$”）]
RG <- read.maimages(files,"spot",wt.fun=wtarea(150))
## End(Not run)[＃结束（不运行）]
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 23:24:34
