cghCall(CGHbase)
cghCall()所属R语言包：CGHbase
Class to contain and describe called array comparative genomic hybridization data.
类包含和描述所谓的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. cghCall class is derived from eSet, and requires the following matrices of equal dimension as assayData members:
aCGH数据和实验的元数据的容器。 cghCalleSet类派生，并要求平等维assayData成员的下列矩阵：
copynumber Log2 copynumber ratios.
copynumber Log2 copynumber比率。
segmented Segmented log2 ratios.
segmented分段的log2比率。
calls Called copynumer values.
calls称为copynumer值。
probloss Loss probabilities as returned by CGHcall.
probloss损失概率返回CGHcall的。
probnorm Normal probabilities as returned by CGHcall.
probnorm，CGHcall恢复正常概率。
probgain Gain probabilities as returned by CGHcall.
probgain增益的概率返回CGHcall的。
probamp Optional amplification probabilities as returned by CGHcall when run with nclass=4.
probamp可选放大作为CGHcall返回的概率与nclass=4运行。
Furthermore, columns named Chromosome, Start, and End are required as featureData members, containing feature position information.
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('cghCall', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], segmented = [matrix], calls = [matrix], probloss = [matrix], probnorm = [matrix], probgain = [matrix], featureData = [AnnotatedDataFrame], ...)
new('cghCall', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], segmented = [matrix], calls = [matrix], probloss = [matrix], probnorm = [matrix], probgain = [matrix], featureData = [AnnotatedDataFrame], ...)
An object of class cghCall is generally obtained as output from CGHcall.
cghCall类的对象一般是获得输出CGHcall。
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 the following matrices
assayData：包含与同等尺寸的矩阵，列数等于nrow(phenoData)。 assayData必须包含以下矩阵
copynumber Log2 copynumber ratios.
copynumber Log2 copynumber比率。
segmented Segmented log2 ratios.
segmented分段的log2比率。
calls Called copynumer values.
calls称为copynumer值。
probloss Loss probabilities as returned by CGHcall.
probloss损失概率返回CGHcall的。
probnorm Normal probabilities as returned by CGHcall.
probnorm，CGHcall恢复正常概率。
probgain Gain probabilities as returned by CGHcall.
probgain增益的概率返回CGHcall的。
probamp Optional amplification probabilities as returned by CGHcall when run with nclass=4.
probamp可选放大作为CGHcall返回的概率与nclass=4运行。
with rows represening array probes and columns representing samples. Additional matrices of identical size (e.g., representing measurement errors) may
与行represening阵探针和列代表样本。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(cghCall), copynumber(cghCall,matrix)<- Access and set elements named copynumber in the AssayData-class
copynumber(cghCall)，copynumber(cghCall,matrix)<-访问集合中元素的名为copynumberAssayData-class
segmented(cghCall), segmented(cghCall,matrix)<- Access and set elements named segmented in the AssayData-class
segmented(cghCall)，segmented(cghCall,matrix)<-访问集合中元素的名为segmentedAssayData-class
calls(cghCall), calls(cghCall,matrix)<- Access and set elements named calls in the AssayData-class
calls(cghCall)，calls(cghCall,matrix)<-访问集合中元素的名为callsAssayData-class
probloss(cghCall), probloss(cghCall,matrix)<- Access and set elements named probloss in the AssayData-class
probloss(cghCall)，probloss(cghCall,matrix)<-访问集合中元素的名为problossAssayData-class
probnorm(cghCall), probnorm(cghCall,matrix)<- Access and set elements named probnorm in the AssayData-class
probnorm(cghCall)，probnorm(cghCall,matrix)<-访问集合中元素的名为probnormAssayData-class
probgain(cghCall), probgain(cghCall,matrix)<- Access and set elements named probgain in the AssayData-class
probgain(cghCall)，probgain(cghCall,matrix)<-访问集合中元素的名为probgainAssayData-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 Create a plot containing log2ratios, segments and call probabilities ordered by chromosomal position. TWO EXTRA OPTIONS PLUS DEFAULTS: dotres=10. Every dotres-th log2-ratio is plotted. dotres=1 plots all data. However, higher values save a lot of space and
绘制创建一个图，包含染色体的位置排列的的log2ratios，分部和呼叫的概率。两个额外的选项加上默认值：dotres = 10。每dotres-TH的log2比绘制。 dotres = 1图的所有数据。然而，更高的价值，节省了大量的空间和
summaryPlot Create a plot summarizing the call probabilities of all samples
summaryPlot总结所有样品的通话概率创建一个图
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, cghRaw-class, cghSeg-class
eSet-class，cghRaw-class，cghSeg-class
举例----------Examples----------
# create an instance of cghCall[创建的cghCall实例]
new("cghCall")
# load an instance of cghCall[加载的cghCall实例]
data(WiltingCalled)
# plot the first sample[绘制第一个样本]
plot(WiltingCalled[,1])
# plot the first chromosome of the first sample[绘制的第一个样品的第一号染色体]
plot(WiltingCalled[chromosomes(WiltingCalled)==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(WiltingCalled[,3:4])
# get the names of the samples[样品名称]
sampleNames(WiltingCalled)
# get the names of the array elements[数组元素的名称]
featureNames(WiltingCalled)
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 2012-2-25 14:29:58
