MethyLumiM-class(methylumi)
MethyLumiM-class()所属R语言包：methylumi
Class "MethyLumiM": for Illumina Methylation microarray data
类“MethyLumiM”Illumina的甲基化芯片的数据：
译者：生物统计家园网 机器人LoveR
描述----------Description----------
MethyLumiM is a class inherited from ExpressionSet-class. It is designed for Illumina Methylation microarray data. The exprs dataMatrix included in the assayData slot of MethyLumiM object includes a matrix of M-values, which is the log2 ratio of methylated and unmethylated probe intensities. The MethyLumiM class include a boxplot function uniquely designed for two-mode histogram data. It also include a coerce function to map from MethyLumi-class, MethyLumiSet-class or other eSet-class inherited object to MethyLumiM class object.
MethyLumiM是ExpressionSet-class继承类。它是专为Illumina的甲基化芯片的数据。 exprs的DataMatrix列入MethyLumiM对象assayData插槽，包括一个矩阵M的值，这是甲基化和甲基化的探针强度的log2比。 MethyLumiM类包括一个盒形图的功能，独特的设计模式直方图数据。它也包括以图要挟功能MethyLumi-class，MethyLumiSet-class或eSet-class继承的对象MethyLumiM类对象。
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("MethyLumiM", exprs, methylated, unmethylated, detection, methylated.N, unmethylated.N, ..., assayData). The "exprs" is a matrix of M-values, which is the log2 ratio of methylated and unmethylated probe intensities; "methylated" and "unmethylated" are intensity matrix measured by methylated and unmethylalted probes of Illumina Infinium methylation microarray; "detection" is the detection p-value outputted by Illumina GenomeStudio software; "methylated.N" and "unmethylated.N" are bead numbers for methylated and unmethylalted probes. "exprs", "methylated" and "unmethylated" information are required for MethyLumiM class. When creating a new MethyLumiM object, the information of "exprs", "methylated", "unmethylated" and "detection" can also be provided directly through "assayData".
创建对象可以通过检测的形式new("MethyLumiM", exprs, methylated, unmethylated, detection, methylated.N, unmethylated.N, ..., assayData)。 “exprs”是一个m值的矩阵，这是log2的甲基化和甲基化的探针强度比;“甲基化”和“甲基化”是由Illumina的Infinium甲基化芯片的甲基化和unmethylalted探针测量的强度矩阵; ;检测“是由Illumina的GenomeStudio软件输出的检测p值;的”methylated.N“和”unmethylated.N“甲基化和unmethylalted探针珠。 “exprs”，“甲基化”和“甲基化”的信息，需要MethyLumiM类。当创建一个新MethyLumiM对象，信息“exprs”，“甲基化”，“甲基化”和“检测”也可以提供直接通过“assayData”。
插槽----------Slots----------
history: Object of class "data.frame" recording the operation history of the LumiBatch object.
history：Object类的"data.frame"记录的LumiBatch对象的经营历史。
controlData: Object of class "MethyLumiQC" to keep the QC probe measurement information.
controlData："MethyLumiQC"保持一流的质量控制探针测量信息的对象。
assayData: Object of class "AssayData", which includes "exprs", "methylated", "unmethylated", "detection", "methylated.N" and "unmethylated.N" data matrix
assayData类"AssayData"，其中包括的“exprs”，“甲基化”，“甲基化”，“检测”，“methylated.N”和“unmethylated.N的对象”数据矩阵
phenoData: Object of class "AnnotatedDataFrame", See eSet-class
phenoData：Object类的"AnnotatedDataFrame"，eSet-class
featureData: Object of class "AnnotatedDataFrame", See eSet-class
featureData：Object类的"AnnotatedDataFrame"，eSet-class
experimentData: Object of class "MIAME", See eSet-class
experimentData：Object类的"MIAME"，eSet-class
annotation: Object of class "character", See eSet-class
annotation：Object类的"character"，eSet-class
protocolData: Object of class "AnnotatedDataFrame", See eSet-class
protocolData：Object类的"AnnotatedDataFrame"，eSet-class
.__classVersion__: Object of class "Versions", See eSet-class
.__classVersion__：Object类的"Versions"，eSet-class
延伸----------Extends----------
Class "ExpressionSet", directly. Class "eSet", by class "ExpressionSet", distance 2. Class "VersionedBiobase", by class "ExpressionSet", distance 3. Class "Versioned", by class "ExpressionSet", distance 4.
类"ExpressionSet"，直接。类"eSet"，类“ExpressionSet”，距离为2。类"VersionedBiobase"，类“ExpressionSet”，距离3。类"Versioned"，类“ExpressionSet”，距离4。
方法----------Methods----------
boxplot signature(x = "MethyLumiM"): plot distribution of M-value
盒形图signature(x = "MethyLumiM")：M的值图分布
coerce signature(from = "eSet", to = "MethyLumiM"): map from MethyLumi-class, MethyLumiSet-class or other eSet-class inherited object to MethyLumiM class object. MethyLumiM object will only keep "exprs", "methylated", "unmethylated" and "detection" data matrix in the assayData.
强制signature(from = "eSet", to = "MethyLumiM")：从图MethyLumi-class，MethyLumiSet-class或其他eSet-class继承的对象MethyLumiM类对象。只MethyLumiM对象将保持“exprs”，“甲基化”，“甲基化”和“检测”数据矩阵中的assayData。
getHistory signature(object = "MethyLumiM"): access the operation history of MethyLumiM object.
getHistorysignature(object = "MethyLumiM")：访问MethyLumiM对象的经营历史。
initialize signature(.Object = "MethyLumiM"): class initialization
初始化signature(.Object = "MethyLumiM")：类初始化
methylated signature(object = "MethyLumiM"): retrieve the data matrix measured by methylated probes
甲基signature(object = "MethyLumiM")：检索甲基化的探针测量数据矩阵
methylated<- signature(object = "MethyLumiM"): set the data matrix measured by methylated probes
甲基化< - signature(object = "MethyLumiM")：设置甲基化的探针测量的数据矩阵
unmethylated signature(object = "MethyLumiM"): retrieve the data matrix measured by unmethylated probes
甲基化signature(object = "MethyLumiM")：检索甲基化探针测量的数据矩阵
unmethylated<- signature(object = "MethyLumiM"): set the data matrix measured by unmethylated probes
甲基化< - signature(object = "MethyLumiM")：设置甲基化探针测量的数据矩阵
methylated.N signature(object = "MethyLumiM"): retrieve the data matrix keeping the number of beads of methylated probes
methylated.Nsignature(object = "MethyLumiM")：检索数据矩阵保持甲基化探针珠
methylated.N<- signature(object = "MethyLumiM"): set the data matrix keeping the number of beads of methylated probes
methylated.N < - signature(object = "MethyLumiM")：设置数据矩阵保持甲基化探针珠
unmethylated.N signature(object = "MethyLumiM"): retrieve the data matrix keeping the number of beads of unmethylated probes
unmethylated.Nsignature(object = "MethyLumiM")：检索数据矩阵保持甲基化探针珠
unmethylated.N<- signature(object = "MethyLumiM"): set the data matrix keeping the number of beads of unmethylated probes
unmethylated.N < - signature(object = "MethyLumiM")：设置数据矩阵保持甲基化探针珠
detection signature(object = "MethyLumiM"): retrieve detection data matrix in AssayData-class
检测signature(object = "MethyLumiM")检索的detection AssayData-class数据矩阵
detection<- signature(object = "MethyLumiM"): set detection data matrix in AssayData-class
检测< - signature(object = "MethyLumiM")：detection数据在AssayData-class矩阵
controlData signature(object = "MethyLumiM"): retrieve the controlData in MethyLumiQC-class
controlDatasignature(object = "MethyLumiM")：检索controlData的MethyLumiQC-class
controlData<- signature(object = "MethyLumiM"): set controlData in MethyLumiQC-class
controlData < - signature(object = "MethyLumiM")：设置controlDataMethyLumiQC-class
作者（S）----------Author(s)----------
Pan DU
参考文献----------References----------
参见----------See Also----------
MethyLumi-class and MethyLumiSet-class
MethyLumi-class和MethyLumiSet-class
举例----------Examples----------
showClass("MethyLumiM")
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。
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发表于 2012-2-26 00:46:29
