cghRegions(CGHbase)
cghRegions()所属R语言包：CGHbase
Class to contain and describe array comparative genomic hybridization regions data.
类包含和描述阵列比较基因组杂交区域的数据。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Container for aCGH regions data and experimental metadata. cghRegions class is derived from eSet, and requires a matrix named regions as assayData member. Furthermore, columns named Chromosome, Start, End, Nclone, and Avedist are required as featureData members, containing region and position information.
的aCGH区域的数据和实验的元数据的容器。 cghRegionseSet类派生，并要求名为regions作为assayData成员的矩阵。此外，列名为Chromosome，Start，End，Nclone，Avedist需要featureData成员，包含区域和位置信息。
延伸----------Extends----------
Directly extends class eSet.
直接延伸类eSet。
创建对象----------Creating Objects----------
new('cghRegions', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], regions = [matrix], featureData = [AnnotatedDataFrame], ...)
new('cghRegions', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], regions = [matrix], featureData = [AnnotatedDataFrame], ...)
An object of this class is generally obtained by running the function CGHregions.
这个类的对象一般是获得运行功能CGHregions。
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 a matrix regions with rows represening regions 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必须包含矩阵与represening代表样本的区域和列行的regions。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, End, Nclone, and Avedist containing region
featureData：AnnotatedDataFrame列Chromosome，Start，End，Nclone，Avedist含区域
experimentData: See eSet
experimentData：见eSet
annotation: See eSet
annotation：见eSet
方法----------Methods----------
Class-specific methods.
类的具体方法。
regions(cghRegions), regions(cghRegions,matrix)<- Access and set elements named regions in the AssayData-class
regions(cghRegions)，regions(cghRegions,matrix)<-访问集合中元素的名为regionsAssayData-class
chromosomes, bpstart, bpend, nclone, avedist Access the region and position
chromosomes，bpstart，bpend，nclone，avedist进入的区域和位置
plot.cghRegions Create a plot displaying chromosomes on the Y-axis and base pair position on the X-axis. A new region is displayed by a slight jump with respect to the previous region. Each region is displayed as a bi-colored segment, the lower and upper part of which correspond to the proportions pl and pg of samples with a loss (red) or gain (green), respectively. The color coding is displayed as well: 1: pl (pg) < 10%; 2: 10% = pl (pg) < 30%; 3:30% = pl (pg) < 50%; 4: pl (pg) = 50%.
plot.cghRegions创建一个图，X轴Y轴和碱基对的位置上显示的染色体。一个新的区域显示，由前区域的轻微跳。作为一个双向色段，下部和上部对应比例PL和PG样品（红色）与亏损或收益（绿色），分别显示每个区域。颜色编码以及显示：1：PL（PG）<10％; 2：10％= PL（PG）<30％; 3:30％= PL（PG）<50％; 4：PL （PG）= 50％。
frequencyPlot Create a frequency plot
frequencyPlot创建一个频率图
See eSet for derived methods. Annotation functionality is not yet supported.
看到eSet派生的方法。注解功能目前还不支持。
作者（S）----------Author(s)----------
Sjoerd Vosse
参见----------See Also----------
eSet, cghRaw-class, cghSeg-class, cghCall-class
eSet，cghRaw-class，cghSeg-class，cghCall-class
举例----------Examples----------
# create an instance of cghRegions[创建的cghRegions实例]
new("cghRegions")
# load an instance of cghRegions[加载的cghRegions实例]
data(WiltingRegions)
# plot all region data[绘制所有区域的数据]
plot(WiltingRegions)
# make a frequency plot[使频率图]
frequencyPlot(WiltingRegions)
# extract the region values[提取区域值]
values <- regions(WiltingRegions)
# get the names of the samples[样品名称]
sampleNames(WiltingRegions)
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 14:30:13
