AffyBatch-class(affy)
AffyBatch-class()所属R语言包：affy
Class AffyBatch
类AffyBatch
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This is a class representation for Affymetrix GeneChip probe level data. The main component are the intensities from multiple arrays of the same CDF type. It extends
这是一个类表示Affymetrix基因芯片探针级数据。的主要成分是从相同的CDF类型的多个阵列的强度。它延伸
类的对象----------Objects from the Class----------
Objects can be created using the function read.affybatch or the wrapper ReadAffy.
可以创建使用功能read.affybatch或包装ReadAffy的对象。
插槽----------Slots----------
cdfName: Object of class character representing the name of CDF file associated with the arrays in the
cdfName：对象类character代表CDF在阵列相关的文件名称
nrow: Object of class integer representing the
nrow：Object类的integer代表
ncol: Object of class integer representing the
ncol：Object类的integer代表
assayData: Object of class AssayData containing the raw data, which will be at minimum a matrix of intensity values. This slot can also hold a matrix of standard errors if the 'sd' argument is set to TRUE in the call to
assayData：Object类的AssayData包含原始数据，这将是最低强度值矩阵。这个插槽也可以按住“SD”参数设置TRUE在调用标准误差矩阵
phenoData: Object of class AnnotatedDataFrame
phenoData类AnnotatedDataFrame：对象
annotation A character string identifying the annotation that may be used for the ExpressionSet
annotation一个字符串，确定可使用ExpressionSet注释
protocolData: Object of class AnnotatedDataFrame
protocolData类AnnotatedDataFrame：对象
featureData Object of class AnnotatedDataFrame
featureDataObject类的AnnotatedDataFrame
experimentData: Object of class "MIAME" containing
experimentData：“MIAME”类的对象，其中包含
.__classVersion__: Object of class Versions describing the R and Biobase version number used to create the
.__classVersion__：Object类的Versions描述的BIOBASE R和版本号使用，以创建
延伸----------Extends----------
Class "eSet", directly.
类"eSet"，直接。
方法----------Methods----------
cdfName signature(object = "AffyBatch"): obtains the
cdfNamesignature(object = "AffyBatch")：获得
pm<- signature(object = "AffyBatch"): replaces the
（下午）< - signature(object = "AffyBatch")：取代
pm signature(object = "AffyBatch"): extracts the pm
下午signature(object = "AffyBatch")：提取下午
mm<- signature(object = "AffyBatch"): replaces the
毫米< - signature(object = "AffyBatch")：替换
mm signature(object = "AffyBatch"): extracts the mm
毫米signature(object = "AffyBatch")：提取毫米
probes signature(object = "AffyBatch", which): extract the perfect match or mismatch probe intensities. Uses which can be
探针signature(object = "AffyBatch", which)：提取的完美匹配或不匹配探针强度。用途
exprs signature(object = "AffyBatch"): extracts the
exprssignature(object = "AffyBatch")：提取
exprs<- signature(object = "AffyBatch", value = "matrix"):
exprs < - signature(object = "AffyBatch", value = "matrix")：
se.exprs signature(object = "AffyBatch"): extracts the
se.exprssignature(object = "AffyBatch")：提取
se.exprs<- signature(object = "AffyBatch", value = "matrix"):
se.exprs < - signature(object = "AffyBatch", value = "matrix")：
[<- signature(x = "AffyBatch"): replaces subsets.
[< - signature(x = "AffyBatch")：替换子集。
[ signature(x = "AffyBatch"): subsets by array.
[signature(x = "AffyBatch")：亚群阵列。
boxplot signature(x = "AffyBatch"): creates a boxplots of log base 2 intensities (pm, mm or both).
盒形图signature(x = "AffyBatch")：创建的log碱基2强度boxplot（下午毫米或两者）。
hist signature(x = "AffyBatch"): creates a plot showing all the histograms of the pm,mm or both data. See
历史signature(x = "AffyBatch")：创建时，毫米或两个数据直方图显示所有的图。见
computeExprSet signature(x = "AffyBatch", summary.method = "character"): For each probe set computes an
computeExprSetsignature(x = "AffyBatch", summary.method = "character")：对于每一个探针集计算
featureNames signature(object = "AffyBatch"): return the probe set names also referred to as the Affymetrix IDs. Notice that one can not assign featureNames. You must do this by changing
featureNamessignature(object = "AffyBatch")：返回探针组还提到Affymetrix公司的ID名。注意不能分配featureNames。你必须做改变
geneNames signature(object="AffyBatch'"): deprecated,
的geneNamessignature(object="AffyBatch'")：弃用
getCdfInfo signature(object = "AffyBatch"): retrieve
getCdfInfosignature(object = "AffyBatch")：检索
image signature(x = "AffyBatch"): creates an image for
形象signature(x = "AffyBatch")：创建一个图像
signature(object = "AffyBatch", which = "character"): returns a list with locations of the probes in each probe set. The affyID corresponding to the probe set to retrieve can be specified in an optional parameter genenames. By default, all the affyIDs are retrieved. The names of the elements in the list returned are the affyIDs. which can be "pm", "mm", or "both". If "both" then perfect match locations are given followed by mismatch locations.
signature(object = "AffyBatch", which = "character")：返回一个列表，在每个探针设置探针的位置。可以指定一个可选的参数genenamesaffyID相应的探针设置检索。默认情况下，被检索所有的affyIDs的。返回列表中的元素的名称是的affyIDs。 which可以是“下午”，“MM”，或“两个”。如果“都”然后完美的比赛地点，其次是不匹配的位置。
signature(object = "AffyBatch", which = "missing") (i.e., calling indexProbes without a "which" argument) is the
signature(object = "AffyBatch", which = "missing")（即indexProbes不“”的说法，称）是
intensity<- signature(object = "AffyBatch"): a
强度< - signature(object = "AffyBatch")：
intensity signature(object = "AffyBatch"): extract the
强度signature(object = "AffyBatch")：提取
length signature(x = "AffyBatch"): returns the number
长度signature(x = "AffyBatch")：返回数字
pmindex signature(object = "AffyBatch"): return the
pmindexsignature(object = "AffyBatch")：返回
mmindex signature(object = "AffyBatch"): return the
mmindexsignature(object = "AffyBatch")：返回
dim signature(x = "AffyBatch"): Row and column dimensions.
朦胧signature(x = "AffyBatch")：行和列的尺寸。
ncol signature(x = "AffyBatch"): An accessor function
NCOLsignature(x = "AffyBatch")：存取功能
nrow signature(x = "AffyBatch"): an accessor function
NROWsignature(x = "AffyBatch")：存取函数
normalize signature(object = "AffyBatch"): a method to normalize. The method accepts an argument method. The default methods is specified in package options
标准化signature(object = "AffyBatch")：normalize方法。该方法接受一个参数method。默认的方法是指定封装选项
normalize.methods signature(object = "AffyBatch"): returns the normalization methods defined for this class. See
normalize.methodssignature(object = "AffyBatch")：返回标准化为这个类定义的方法。见
probeNames signature(object = "AffyBatch"): returns
probeNamessignature(object = "AffyBatch")：返回
probeset signature(object = "AffyBatch",genenames=NULL, locations=NULL): Extracts ProbeSet objects related to the probe sets given in genenames. If an alternative set of locations defining pms and mms a list with those locations should
probesetsignature(object = "AffyBatch",genenames=NULL, locations=NULL)：提取ProbeSet探针的对象设置在genenames给予。如果一个地点的另一套定义PMS和MMS这些地点的列表应
bg.correct signature(object = "AffyBatch", method="character") applies background correction methods defined by
bg.correctsignature(object = "AffyBatch", method="character")定义背景校正方法应用于
updateObject signature(object = "AffyBatch", ..., verbose=FALSE): update, if necessary, an object of class AffyBatch to its current class definition. verbose=TRUE
updateObjectsignature(object = "AffyBatch", ..., verbose=FALSE)：更新，如果必要的话，当前的类定义一个类AffyBatch的对象。 verbose=TRUE
注意----------Note----------
This class is better described in the vignette.
更好地描述这个类中的小插曲。
参见----------See Also----------
related methods merge.AffyBatch, pairs.AffyBatch, and
相关的方法merge.AffyBatch，pairs.AffyBatch，
举例----------Examples----------
if (require(affydata)) {
## load example[＃加载的例子]
data(Dilution)
## nice print[＃不错的打印]
print(Dilution)
pm(Dilution)[1:5,]
mm(Dilution)[1:5,]
## get indexes for the PM probes for the affyID "1900_at" [＃得到，为的affyID“1900_at”下午探针指标]
mypmindex <- pmindex(Dilution,"1900_at")
## same operation using the primitive[＃相同的操作使用原始]
mypmindex <- indexProbes(Dilution, which="pm", genenames="1900_at")[[1]]
## get the probe intensities from the index[＃从索引中得到的探针强度。]
intensity(Dilution)[mypmindex, ]
description(Dilution) ##we can also use the methods of eSet[＃我们也可以使用ESET的方法]
sampleNames(Dilution)
abstract(Dilution)
}
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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。
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发表于 2012-2-25 11:25:01
