MethyLumi-class(methylumi)
MethyLumi-class()所属R语言包:methylumi
The base class for storing Illumina Methylation data
Illumina的甲基化数据存储的基类
译者:生物统计家园网 机器人LoveR
描述----------Description----------
This class inherits from eSet from the Biobase package and is used as a base class for the other two methylumi classes,
这个类继承从eSet从BIOBASE包和用于其他两个methylumi类作为基类,
类的对象----------Objects from the Class----------
The MethyLumi class is a virtual class and is not meant to be instantiated. Instead, one should instantiate a MethyLumiSet or a MethyLumiQC object.
类MethyLumi是一个虚拟类,是注定不会被实例化。相反,一个实例MethyLumiSet或MethyLumiQC对象。
插槽----------Slots----------
assayData: Object of class "AssayData"
assayData类"AssayData":对象
phenoData: Object of class "AnnotatedDataFrame"
phenoData类"AnnotatedDataFrame":对象
featureData: Object of class "AnnotatedDataFrame" that will hold the annotation columns
featureData:"AnnotatedDataFrame"类的对象,将持有的注解列
experimentData: Object of class "MIAME"
experimentData类"MIAME":对象
annotation: Object of class "character"; note that this slot is not currently used, but may be used in the
annotation:Object类的"character";注意到,目前没有使用这个插槽,但可以用在
.__classVersion__: Object of class "Versions"
.__classVersion__类"Versions":对象
延伸----------Extends----------
Class "eSet", directly. Class "VersionedBiobase", by class "eSet", distance 2. Class "Versioned", by class "eSet", distance 3.
类"eSet",直接。类"VersionedBiobase",“ESET”级,距离为2。类"Versioned",“ESET”级,距离3。
方法----------Methods----------
pvals<- signature(object = "MethyLumi", value = "matrix"): Set the assayData slot of the same name and stores the P-values from BeadStudio
pvals < - signature(object = "MethyLumi", value = "matrix"):设置的同名assayData插槽和存储BeadStudio P值
pvals signature(object = "MethyLumi"): Get the assayData slot of the same name
pvalssignature(object = "MethyLumi"):获取相同的名称assayData插槽
betas<- signature(object = "MethyLumi", value = "matrix"): Set the assayData slot of the same name and represents the methylation values for the samples, analogous to exprs() in gene expression data.
的贝塔< - signature(object = "MethyLumi", value = "matrix"):设置的同名assayData插槽和代表样品的甲基化值,类似于exprs(在基因表达数据)。
betas signature(object = "MethyLumi"): Get the assayData slot of the same name
贝塔signature(object = "MethyLumi"):获取相同的名称assayData插槽
methylated<- signature(object = "MethyLumi", value = "matrix"): Set the assayData slot that represents the Methylated single-channel signal
甲基化< - signature(object = "MethyLumi", value = "matrix"):设置assayData插槽,甲基化的单声道信号
methylated signature(object = "MethyLumi"): Get the assayData slot that represents the Methylated single-channel signal
甲基signature(object = "MethyLumi"):获取的assayData的插槽,甲基化的单声道信号
unmethylated<- signature(object = "MethyLumi", value = "matrix"): Set the assayData slot that represents the Unmethylated single-channel signal
甲基化< - signature(object = "MethyLumi", value = "matrix"):设置assayData槽表示甲基化的单声道信号
unmethylated signature(object = "MethyLumi"): Get the assayData slot that represents the Unmethylated single-channel signal
甲基化signature(object = "MethyLumi"):获取的assayData的槽表示甲基化的单声道信号
controlTypes signature(object = "MethyLumi"
controlTypessignature(object = "MethyLumi"
: Find the unique control type beeds in the QCdata slot.
:寻找独特的控制型beeds的在QCdata插槽。
qcplot signature(object = "MethyLumi",what,...): Plot of QC data. This plot can be useful for diagnosing the problems associated with specific samples or arrays. The value for "what" is one of the control types (which can be found by using controlTypes() on the object.
qcplotsignature(object = "MethyLumi",what,...):图QC数据。此图可用于诊断与特定样品或阵列相关的问题。 “什么”的值是一个控制类型(可以通过使用controlTypes()对象发现。
summary signature(object = "MethyLumi",...)
摘要signature(object = "MethyLumi",...)
: summary method for MethyLumi objects.
:简易方法MethyLumi对象。
作者(S)----------Author(s)----------
Sean Davis <sdavis2@mail.nih.gov>
参见----------See Also----------
methylumiR, MethyLumiSet, MethyLumiQC, eSet
methylumiR,MethyLumiSet,MethyLumiQC,eSet
举例----------Examples----------
## The class structure[#类结构]
showClass("MethyLumi")
## read in some data[#读取一些数据]
## Read in sample information[#样品信息阅读]
samps <- read.table(system.file("extdata/samples.txt",
package = "methylumi"),sep="\t",header=TRUE)
## Perform the actual data reading[#执行实际的数据读]
## This is an example of reading data from a [#这是一个从读取数据的例子]
## Sentrix Array format file (actually two files,[的#Sentrix阵列格式的文件(实际上是两个文件,]
## one for data and one for QC probes)[一个用于数据和质控探针)]
mldat <- methylumiR(system.file('extdata/exampledata.samples.txt',
package='methylumi'),
qcfile=system.file('extdata/exampledata.controls.txt',
package="methylumi"),
sampleDescriptions=samps)
mldat
## Get history information[#获取历史信息。]
getHistory(mldat)
## Get QC data, which is another eSet-derived object[#获取QC数据,这是另一个ESET派生的对象]
QCdata(mldat)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注:
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