cghSeg(CGHbase)
cghSeg()所属R语言包：CGHbase
Class to contain and describe segmented array comparative genomic hybridization data.
类包含和描述分割阵列比较基因组杂交数据。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Container for aCGH data and experimental metadata. cghSeg class is derived from eSet, and requires a matrix named copynumber as well as a matrix named segmented as assayData members of equal dimensions. Furthermore, columns named Chromosome, Start, and End are required as featureData members, containing feature position information.
aCGH数据和实验的元数据的容器。 派生cghSeg类eSet，需要一个矩阵名为copynumber以及矩阵名为segmented作为平等尺寸assayData的成员。此外，列名为Chromosome，Start，功能End需要featureData成员，包含位置信息。
延伸----------Extends----------
Directly extends class eSet.
直接延伸类eSet。
创建对象----------Creating Objects----------
new('cghSeg', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], segmented = [matrix], featureData = [AnnotatedDataFrame], ...)
new('cghSeg', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], segmented = [matrix], featureData = [AnnotatedDataFrame], ...)
An object of class cghSeg is generally obtained as output from segmentData.
cghSeg类的对象一般是获得输出segmentData。
插槽----------Slots----------
Inherited from eSet:
继承自eSet
assayData: Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). assayData must contain matrices copynumber and segmented with rows represening array probes and columns representing samples. Additional matrices of identical size (e.g., representing measurement errors) may
assayData：包含与同等尺寸的矩阵，列数等于nrow(phenoData)。 assayData必须包含矩阵copynumber和segmentedrepresening阵探针和列代表样本的行。相同大小的附加矩阵（例如，代表测量误差）
phenoData: See eSet
phenoData：见eSet
featureData: An AnnotatedDataFrame with columns Chromosome, Start, and End containing array element position
featureData：AnnotatedDataFrame同列Chromosome，Start，End包含数组元素的位置
experimentData: See eSet
experimentData：见eSet
annotation: See eSet
annotation：见eSet
方法----------Methods----------
Class-specific methods.
类的具体方法。
copynumber(cghSeg), copynumber(cghSeg,matrix)<- Access and set elements named copynumber in the AssayData-class
copynumber(cghSeg)，copynumber(cghSeg,matrix)<-访问集合中元素的名为copynumberAssayData-class
segmented(cghSeg), segmented(cghSeg,matrix)<- Access and set elements named segmented in the AssayData-class
segmented(cghSeg)，segmented(cghSeg,matrix)<-访问集合中元素的名为segmentedAssayData-class
chromosomes, bpstart, bpend Access the chromosomal positions stored in featureData
chromosomes，bpstart，bpend访问featureData存储的染色体位置
plot.cghSeg Create a plot containing log2ratios and segments ordered by chromosomal position
plot.cghSeg创建一个图含有log2ratios和染色体位置下令段
See eSet for derived methods.
看到eSet派生的方法。
作者（S）----------Author(s)----------
Sjoerd Vosse
参见----------See Also----------
eSet-class, ExpressionSet-class, cghRaw-class, cghCall-class
eSet-class，ExpressionSet-class，cghRaw-class，cghCall-class
举例----------Examples----------
# create an instance of cghSeg[创建的cghSeg实例]
new("cghSeg")
# load an instance of cghSeg[加载的cghSeg实例]
data(WiltingSeg)
# plot the first sample[绘制第一个样本]
# plot(WiltingSeg[,1])[图（WiltingSeg [1]）]
# first three chromosomes[第3染色体]
# plot(WiltingSeg[chromosomes(WiltingSeg)==1,1])[图（WiltingSeg染色体（WiltingSeg）的== 1,1]）]
# get the copynumber values of the third and fourth sample[获得的第三个和第四个样本copynumber值]
log2ratios <- copynumber(WiltingSeg[,3:4])
# get the names of the samples[样品名称]
sampleNames(WiltingSeg)
# get the names of the array elements[数组元素的名称]
featureNames(WiltingSeg)
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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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 14:30:23
