read.affybatch(affy)
read.affybatch()所属R语言包：affy
Read CEL files into an AffyBatch
CEL文件到AffyBatch读取
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Read CEL files into an Affybatch.
到Affybatch读取CEL文件。
用法----------Usage----------
read.affybatch(..., filenames = character(0),
phenoData = new("AnnotatedDataFrame"),
description = NULL,
notes = "",
compress = getOption("BioC")$affy$compress.cel,
rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE,
verbose = FALSE,sd=FALSE, cdfname = NULL)
ReadAffy(..., filenames=character(0),
widget=getOption("BioC")$affy$use.widgets,
compress=getOption("BioC")$affy$compress.cel,
celfile.path=NULL,
sampleNames=NULL,
phenoData=NULL,
description=NULL,
notes="",
rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE,
verbose=FALSE,sd=FALSE, cdfname = NULL)
参数----------Arguments----------
参数：...
file names separated by comma.
用逗号分隔的文件名。
参数：filenames
file names in a character vector.
文件名称中的字符向量。
参数：phenoData
an AnnotatedDataFrame object, a character of length one, or a data.frame.
AnnotatedDataFrame对象，长度，或characterdata.frame。
参数：description
a MIAME object.
MIAME对象。
参数：notes
notes.
笔记。
参数：compress
are the CEL files compressed?
CEL文件压缩？
参数：rm.mask
should the spots marked as 'MASKS' set to NA?
斑点标示为“面具”设置为NA？
参数：rm.outliers
should the spots marked as 'OUTLIERS' set to NA?
斑点标示为“离群”设置NA？
参数：rm.extra
if TRUE, then overrides what is in rm.mask and rm.oultiers.
TRUE如果，然后覆盖在rm.mask和rm.oultiers是什么。
参数：verbose
verbosity flag.
冗长的标志。
参数：widget
a logical specifying if widgets should be used.
逻辑指定是否应使用部件。
参数：celfile.path
a character denoting the path ReadAffy should look for cel files.
字符表示的路径ReadAffy应该看看为CEL档案。
参数：sampleNames
a character vector of sample names to be used in the AffyBatch.
特征向量的样本名被用来在AffyBatch。
参数：sd
should the standard deviation values in the CEL file be read in? Since these are typically not used default is not to read them in. This also save lots of memory.
在CEL文件的标准偏差值应在阅读吗？由于这些通常不使用默认情况下是不读。这还可以节省大量内存。
参数：cdfname
used to specify the name of an alternative cdf package. If set to NULL, then the usual cdf package based on Affymetrix's mappings will be used.
用于指定替代的CDF包的名称。如果设置为NULL，然后根据Affymetrix公司的映射通常CDF包将被用于。
Details
详情----------Details----------
ReadAffy is a wrapper for read.affybatch that permits the user to read in phenoData, MIAME information, and CEL files using widgets. One can also define files where to read phenoData and MIAME information.
ReadAffy是一个包装read.affybatch，允许用户在phenoData读，的MIAME信息，并使用部件CEL文件。还可以定义文件阅读phenoData MIAME信息。
If the function is called with no arguments ReadAffy() all the CEL files in the working directory are read and put into an AffyBatch. However, the arguments give the user great flexibility.
如果该函数不带参数调用ReadAffy()工作目录中的所有CEL文件阅读并投入AffyBatch。然而，参数为用户提供了极大的灵活性。
If phenoData is a character vector of length 1, the function read.AnnotatedDataFrame is called to read a file of that name and produce the AnnotationDataFrame object with the sample metadata. If phenoData is a data.frame, it is converted to an AnnotatedDataFrame. If it is NULL and widget=FALSE (widget=TRUE is not currently supported), then a default object of class AnnotatedDataFrame is created, whose pData is a data.frame with rownames being the names of the CEL files, and with one column sample with an integer index.
如果phenoData是一个长度为1的特征向量，函数read.AnnotatedDataFrame被称为读这个名字的文件，并产生AnnotationDataFrame样本元数据的对象。如果phenoData是1 data.frame，它被转换为一个AnnotatedDataFrame。如果是NULL和widget=FALSE（widget=TRUE目前不支持），然后默认对象的类AnnotatedDataFrame创建的，其pData是一个数据。帧rownames是CEL文件的名称，并与一列sample一个整数索引。
AllButCelsForReadAffy is an internal function that gets called by ReadAffy. It gets all the information except the cel intensities.
AllButCelsForReadAffy是一个内部功能得到ReadAffy的叫。它得到以外的所有的CEL强度的信息。
description is read using read.MIAME. If a character is given, then it tries to read the file with that name to obtain a MIAME instance. If left NULL but widget=TRUE, then widgets are used. If left NULL and widget=FALSE, then an empty instance of MIAME is created.
description使用read.MIAME被读取。如果一个字符，然后它尝试读取这个名字的文件，以取得MIAME实例。如果左NULL但是widget=TRUE，然后部件都使用。如果左NULL和widget=FALSE，则的MIAME空实例被创建。
值----------Value----------
An AffyBatch object.
AffyBatch对象。
作者（S）----------Author(s)----------
Ben Bolstad <a href="mailto:bmb@bmbolstad.com">bmb@bmbolstad.com</a> (read.affybatch),
Laurent Gautier, and Rafael A. Irizarry (ReadAffy)
参见----------See Also----------
AffyBatch
AffyBatch
举例----------Examples----------
if(require(affydata)){
celpath <- system.file("celfiles", package="affydata")
fns <- list.celfiles(path=celpath,full.names=TRUE)
cat("Reading files:\n",paste(fns,collapse="\n"),"\n")
##read a binary celfile[＃读取二进制celfile]
abatch <- ReadAffy(filenames=fns[1])
##read a text celfile[＃读取文本celfile]
abatch <- ReadAffy(filenames=fns[2])
##read all files in that dir[＃读取该目录的所有文件]
abatch <- ReadAffy(celfile.path=celpath)
}
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 11:30:22
