MethyLumiSet-class(methylumi)
MethyLumiSet-class()所属R语言包：methylumi
Class "MethyLumiSet" for containing Illumina methylation data
类的“MethyLumiSet”含有Illumina的甲基化数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class inherits from the MethyLumi class (and therefore, from eSet in Biobase) and is designed to hold both the
这个类继承自MethyLumi类（因此，从ESET在BIOBASE）举行
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("MethyLumiSet", assayData, phenoData, featureData, experimentData, annotation, betas). An object of this type is the main storage class for methylation data from Illumina. Subsetting, etc., works as normal (rows represent genes, columns represent samples). There is also a rudimentary history tracking system that is modeled after that from the lumi package.
创建对象可以通过检测的形式new("MethyLumiSet", assayData, phenoData, featureData, experimentData, annotation, betas)。这种类型的对象是从Illumina公司的甲基化数据的主要存储类。子集等，工作正常（行表示基因，列代表样本）。还有一个基本的历史跟踪系统后，从LUMI包为蓝本。
插槽----------Slots----------
QC: Object of class "QCDataOrNULL", containing
QC：Object类的"QCDataOrNULL"，包含
history: Object of class "data.frame",
history：Object类的"data.frame"，
assayData: Object of class AssayData
assayData类AssayData：对象
phenoData: Object of class AnnotatedDataFrame
phenoData类AnnotatedDataFrame ：对象
featureData: Object of class
featureData：对象类
experimentData: Object of class MIAME
experimentData类MIAME：对象
annotation: Object of class "character", not
annotation类"character"，不对象
.__classVersion__: Object of class "Versions"
.__classVersion__类"Versions"：对象
protocolData: Object of class "AnnotatedDataFrame" that contains protocol information,
protocolData："AnnotatedDataFrame"类的对象，其中包含的协议信息，
延伸----------Extends----------
Class "MethyLumi", directly. Class "methylData", directly. Class "eSet", by class "MethyLumi", distance 2. Class "VersionedBiobase", by class "MethyLumi", distance 3. Class "Versioned", by class "MethyLumi", distance 4.
类"MethyLumi"，直接。类"methylData"，直接。类"eSet"，类“MethyLumi”，距离为2。类"VersionedBiobase"，类“MethyLumi”，距离3。类"Versioned"，类“MethyLumi”，距离4。
方法----------Methods----------
[ signature(x = "MethyLumiSet"): subsetting, genes as rows, samples as columns
[signature(x = "MethyLumiSet")：子集，作为行的基因，为列样本
betas<- signature(object = "MethyLumiSet", value = "matrix"): Set the assayData slot of the same name
贝塔< - signature(object = "MethyLumiSet", value = "matrix")：设置的同名assayData插槽
betas signature(object = "MethyLumiSet"): Get the assayData slot of the same name
贝塔signature(object = "MethyLumiSet")：获取相同的名称assayData插槽
boxplot signature(x = "MethyLumiSet"): boxplot of all
盒形图signature(x = "MethyLumiSet")：所有盒形图
combine signature(x = "MethyLumiSet", y = "MethyLumiSet")
结合signature(x = "MethyLumiSet", y = "MethyLumiSet")
corplot signature(x = "MethyLumiSet")
corplotsignature(x = "MethyLumiSet")
exprs signature(object = "MethyLumiSet"): returns m-values
exprssignature(object = "MethyLumiSet")：返回m值
getHistory signature(object = "MethyLumiSet"): returns
getHistorysignature(object = "MethyLumiSet")：返回
hist signature(x = "MethyLumiSet"): histogram of the
历史signature(x = "MethyLumiSet")：直方图
initialize signature(.Object = "MethyLumiSet")
初始化signature(.Object = "MethyLumiSet")
pairs signature(x = "MethyLumiSet"): pairs plot of the
对signature(x = "MethyLumiSet")：对图
plotSampleIntensities signature(x = "MethyLumiSet"): The intensities as output by the Beadstudio software often show a considerable amount of dye bias. This method shows a graphical example of this dye bias. In short, for each of the Cy3 and Cy5 channels, a cutoff in beta is used to calculate which Cy3 and Cy5 values should be plotted at high-methylation and low-methylation status. Any offset between Cy3 and Cy5 when plotted in this way likely represents dye bias and will lead to biases in the estimate
plotSampleIntensitiessignature(x = "MethyLumiSet")：作为输出由Beadstudio软件的强度往往会表现出相当数量的染料偏见。这种方法显示了这种染料偏见的图形化的例子。总之，每个Cy3和Cy5通道，在测试的截止用来计算Cy3和Cy5值应绘制在高甲基化和低甲基化状态。 Cy3和Cy5之间的任何偏移时，在这种方式绘制，可能代表染料偏见，并会导致估计偏差
QCdata<- signature(object = "MethyLumiSet", value =
QCdata < - 的<code>签名（对象=“MethyLumiSet”，值=
QCdata signature(object = "MethyLumiSet"): retrieve
QCdatasignature(object = "MethyLumiSet")：检索
show signature(object = "MethyLumiSet")
显示signature(object = "MethyLumiSet")
methylated<- signature(object = "MethyLumiSet", value =
甲基化< - 的<code>签名（对象=“MethyLumiSet”，值=
methylated signature(object = "MethyLumiSet"): Get the assayData slot associated with methylated intensity
甲基signature(object = "MethyLumiSet")：获取的assayData的槽相关的甲基化强度
unmethylated<- signature(object = "MethyLumiSet", value = "matrix"): Set the assayData slot associated with unmethylated intensity
甲基化< - signature(object = "MethyLumiSet", value = "matrix")：设置assayData插槽相关的甲基化强度
unmethylated signature(object = "MethyLumiSet"): Get the assayData slot associated with unmethylated intensity
甲基化signature(object = "MethyLumiSet")：获取的assayData的强度与甲基化相关的插槽
qcplot signature(object = "MethyLumiSet", what, ...):
qcplotsignature(object = "MethyLumiSet", what, ...)：
controlTypes signature(object = "MethyLumiSet"): determine the character vector of control types from the QCdata
controlTypessignature(object = "MethyLumiSet")：决定从QCdata的控制类型的特征向量
Cy3.N signature(object = "MethyLumiSet"): ...
Cy3.Nsignature(object = "MethyLumiSet")...
Cy5.N signature(object = "MethyLumiSet"): ...
Cy5.Nsignature(object = "MethyLumiSet")...
combine27k450k signature(x = "MethyLumiSet", y = "MethyLumiSet"): ...
combine27k450ksignature(x = "MethyLumiSet", y = "MethyLumiSet")...
controlData signature(object = "MethyLumiSet"): ...
controlDatasignature(object = "MethyLumiSet")...
controlData<- signature(object = "MethyLumiSet", value = "MethyLumiQC"): ...
controlData < - signature(object = "MethyLumiSet", value = "MethyLumiQC")...
featureFilter signature(eset = "MethyLumiSet"): ...
featureFiltersignature(eset = "MethyLumiSet")...
intensities.IB signature(x = "MethyLumiSet", channel = "character"): ...
intensities.IBsignature(x = "MethyLumiSet", channel = "character")...
intensities.IB signature(x = "MethyLumiSet", channel = "missing"): ...
intensities.IBsignature(x = "MethyLumiSet", channel = "missing")...
intensities.M signature(x = "MethyLumiSet", channel = "character"): ...
intensities.Msignature(x = "MethyLumiSet", channel = "character")...
intensities.M signature(x = "MethyLumiSet", channel = "missing"): ...
intensities.Msignature(x = "MethyLumiSet", channel = "missing")...
intensities.OOB.allelic signature(x = "MethyLumiSet", channel = "character", allele = "character"): ...
intensities.OOB.allelicsignature(x = "MethyLumiSet", channel = "character", allele = "character")...
intensities.OOB.allelic signature(x = "MethyLumiSet", channel = "missing", allele = "missing"): ...
intensities.OOB.allelicsignature(x = "MethyLumiSet", channel = "missing", allele = "missing")...
intensities.OOB signature(x = "MethyLumiSet", channel = "character"): ...
intensities.OOBsignature(x = "MethyLumiSet", channel = "character")...
intensities.OOB signature(x = "MethyLumiSet", channel = "missing"): ...
intensities.OOBsignature(x = "MethyLumiSet", channel = "missing")...
intensities.U signature(x = "MethyLumiSet", channel = "character"): ...
intensities.Usignature(x = "MethyLumiSet", channel = "character")...
intensities.U signature(x = "MethyLumiSet", channel = "missing"): ...
intensities.Usignature(x = "MethyLumiSet", channel = "missing")...
intensitiesByChannel signature(object = "MethyLumiSet"): ...
intensitiesByChannelsignature(object = "MethyLumiSet")：...
negctls.stderr signature(object = "MethyLumiSet", channel = "character"): ...
negctls.stderrsignature(object = "MethyLumiSet", channel = "character")：...
negctls.stderr signature(object = "MethyLumiSet", channel = "missing"): ...
negctls.stderrsignature(object = "MethyLumiSet", channel = "missing")：...
negctls signature(object = "MethyLumiSet", channel = "character"): ...
negctlssignature(object = "MethyLumiSet", channel = "character")...
negctls signature(object = "MethyLumiSet", channel = "missing"): ...
negctlssignature(object = "MethyLumiSet", channel = "missing")...
negnorm signature(object = "MethyLumiSet", channel = "character"): ...
negnormsignature(object = "MethyLumiSet", channel = "character")...
negnorm signature(object = "MethyLumiSet", channel = "missing"): ...
negnormsignature(object = "MethyLumiSet", channel = "missing")...
normctls signature(object = "MethyLumiSet"): ...
normctlssignature(object = "MethyLumiSet")...
plotSampleIntensities signature(x = "MethyLumiSet"): ...
plotSampleIntensitiessignature(x = "MethyLumiSet")...
probeNAs signature(object = "MethyLumiSet"): ...
probeNAssignature(object = "MethyLumiSet")...
sampleNAs signature(object = "MethyLumiSet"): ...
sampleNAssignature(object = "MethyLumiSet")...
total.intensity signature(object = "MethyLumiSet"): ...
total.intensitysignature(object = "MethyLumiSet")：...
varFilter signature(eset = "MethyLumiSet"): ...
varFiltersignature(eset = "MethyLumiSet")...
作者（S）----------Author(s)----------
Sean Davis & Tim Triche, Jr.
参见----------See Also----------
methylumiR, normalizeMethyLumiSet, methylumIDAT, MethyLumiQC, eSet
methylumiR，normalizeMethyLumiSet，methylumIDAT，MethyLumiQC，eSet
举例----------Examples----------
showClass("MethyLumiSet")
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 00:46:48
