read.marrayRaw(marray)
read.marrayRaw()所属R语言包：marray
Create objects of class "marrayRaw"
创建对象的类“marrayRaw”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function reads in cDNA microarray data from a directory and creates objects of class "marrayRaw" from spot quantification data files obtained from image analysis software or databases.
此功能cDNA微阵列数据读取从一个目录，并创建对象类"marrayRaw"从现场定量图像分析软件或数据库获得的数据文件。
用法----------Usage----------
read.marrayRaw(fnames, path=".", name.Gf=NULL, name.Gb=NULL, name.Rf=NULL,
name.Rb=NULL,name.W=NULL, layout=NULL, gnames=NULL, targets=NULL,
notes=NULL, skip=NULL, sep=" ", quote="\"", DEBUG=FALSE, ...)
read.GenePix(fnames = NULL, path = NULL, name.Gf = "F532 Median",
name.Gb ="B532 Median", name.Rf = "F635 Median", name.Rb = "B635 Median",
name.W ="Flags", layout = NULL, gnames = NULL, targets = NULL,
notes = NULL, skip=NULL, sep = " ", quote = "\"", DEBUG=FALSE, ...)
read.SMD(fnames = NULL, path = NULL, name.Gf = "Ch1 Intensity (Median)",
name.Gb = "Ch1 Background (Median)", name.Rf = "Ch2 Intensity (Median)",
name.Rb = "Ch2 Background (Median)", name.W = NULL, info.id = c("Name",
"Clone ID"), layout = NULL, gnames = NULL, targets = NULL, notes = NULL, skip = NULL, sep = "\t", quote = "\"", DEBUG=FALSE, ...)
read.Spot(fnames = NULL, path = ".", name.Gf = "Gmean", name.Gb =
"morphG", name.Rf = "Rmean", name.Rb = "morphR",name.W = NULL, layout =
NULL, gnames = NULL, targets = NULL, notes = NULL, skip = NULL, sep = "\t", quote = "\"", DEBUG=FALSE, ...)
read.Agilent(fnames = NULL, path=NULL, name.Gf = "gMedianSignal", name.Gb = "gBGMedianSignal", name.Rf = "rMedianSignal", name.Rb = "rBGMedianSignal", name.W= NULL, layout = NULL, gnames = NULL, targets = NULL, notes=NULL, skip=NULL, sep="\t", quote="\"", DEBUG=FALSE, info.id=NULL, ...)
widget.marrayRaw(ext = c("spot", "xls", "gpr"), skip = 0, sep = "\t", quote = "\"", ...)
参数----------Arguments----------
参数：fnames
a vector of character strings containing the file names of each spot quantification data file. These typically end in .spot for the software Spot or .gpr for the software GenePix.
每个点的量化数据文件的文件名字符串的字符包含的向量。这些典型的高端.spot软件Spot或.gpr软件GenePix。
参数：path
a character string representing the data directory. By default this is set to the current working directory ("."). In the case where fnames contains the full path name, path should be set to NULL.
一个字符串，代表数据目录。默认情况下，这是设置为当前工作目录（“。”）。 fnames包含完整路径名的情况下，路径应设置为NULL。
参数：name.Gf
character string for the column header for green foreground intensities.
绿色前景强度列标题的字符串。
参数：name.Gb
character string for the column header for green background intensities.
绿色背景强度列标题的字符串。
参数：name.Rf
character string for the column header for red foreground intensities.
红色前景强度列标题的字符串。
参数：name.Rb
character string for the column header for red background intensities.
字符串列标题为红色背景强度。
参数：name.W
character string for the column header for spot quality weights.
现场质量权重的列标题的字符串。
参数：layout
object of class "marrayLayout", containing microarray layout parameters.
对象的类"marrayLayout"，含有芯片的布局参数。
参数：gnames
object of class "marrayInfo" containing probe sequence information.
对象的类"marrayInfo"含探针序列信息。
参数：targets
object of class "marrayInfo" containing target sample information.
对象的类"marrayInfo"含目标样本信息。
参数：notes
object of class "character", vector of explanatory text.
对象类"character"，解释性文字向量。
参数：info.id
object of class "character", vector containing the name of the colums of the SMD file containing oligo information you want to retrieve. By default, this is set to read Homo sapiens data. You may need to modify this argument if your are working on another genome.
类对象"character"，向量含有低聚你想要的信息检索的SMD文件colums的名称。默认情况下，这是设置读取数据智人。如果您在另一个基因组的工作，你可能需要修改此参数。
参数：skip
the number of lines of the data file to skip before beginning to read in data.
行的数据文件数量跳过前开始读取数据。
参数：sep
the field separator character. Values on each line of the file are separated by this character. The default is to read a tab delimited file.
字段分隔符。文件的每一行的值是通过这个角色分离。默认是读取一个制表符分隔的文件。
参数：quote
the set of quoting characters. By default, this is disabled by setting quote="\"".
引用字符集。默认情况下，这是通过设置quote="\""禁用。
参数：ext
a characters string representing suffix of different image analysis output files.
字符的字符串代表不同的图像分析输出文件的后缀。
参数：DEBUG
a logical value, if TRUE, a series of echo statements will be printed.
一个逻辑值，如果属实，将一系列echo语句打印。
参数：...
further arguments to scan.
scan进一步的论据。
值----------Value----------
An object of class "marrayRaw".
对象类"marrayRaw"。
作者（S）----------Author(s)----------
Jean Yang, <a href="mailto:yeehwa@stat.berkeley.edu">yeehwa@stat.berkeley.edu</a>
参考文献----------References----------
<h3>See Also</h3> <code>scan</code>, <code>read.marrayLayout</code>,
举例----------Examples----------
datadir <- system.file("swirldata", package="marray")
## Quick guide[＃快速指南]
swirl.targets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt"))
data <- read.Spot(path=datadir, targets=swirl.targets)
## Alternate commands[＃替代命令]
skip <- grep("Row", readLines(file.path(datadir,"fish.gal"), n=100)) - 1
swirl.layout <- read.marrayLayout(ngr=4, ngc=4, nsr=22, nsc=24)
swirl.targets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt"))
swirl.gnames <- read.marrayInfo(file.path(datadir, "fish.gal"),
info.id=4:5, labels=5, skip=skip)
x <- maInfo(swirl.gnames)[,1]
y <- rep(0, maNspots(swirl.layout))
y[x == "control"] <- 1
slot(swirl.layout, "maControls") <- as.factor(y)
fnames <- dir(path=datadir,pattern="spot")
swirl<- read.Spot(fnames, path=datadir,
layout = swirl.layout,
gnames = swirl.gnames,
targets = swirl.targets)
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 2012-2-26 00:21:47
