heatMapMeth(methVisual)
heatMapMeth()所属R语言包：methVisual
HeatMap diagram over methylation data
过甲基化数据热图图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
HeatMap diagram of methylation classes over CpG position and sequence level
甲基类的CpG位置和序列水平的热图图
用法----------Usage----------
heatMapMeth(methData,file)
参数----------Arguments----------
参数：methData
List; contains information on the pairwise alignments, and methylated CpG motifs
名单;包含成对的路线，和甲基化的CpG基序的信息
参数：file
optionally, quoted character string for specification of path and file name for saving the result. By default, the result file's format is .pdf. If argument is omitted, screen output is provided only.
可选，引用规范的路径和文件名保存结果的字符字符串。默认情况下，结果文件的格式是PDF。如果省略参数，屏幕输出。
Details
详情----------Details----------
Clustering is a prominent method for visualizing and studying groups of similar features, and is also widely used for the analysis of microarrays. In the case of analyzing DNA methylation datasets the matrix to be explored is a I*J binary matrix, were I are the clone sequences and J are the CpG positions. Every index in this matrix has the value 1 for methylated or 0 for non methylated CpG sites. Providing a hierarchical clustering option based on the quality checked methylation data can be useful in finding clusters in the explored data in two dimensions, of the methylation state of CpG sites (J) and for distribution of methylation state over explored clone sequences (I). Very importantly, one has to keep in mind, that this method does not take into account the genomic ordering of CpG sites. Clustering methods can be also useful in quality control check. Observing clones from the same PCR product in different clusters can point to bad quality clone sequences. The clustering method which was used in methVisual R package is the heatmap() function from stat package which is a color image with two dendrograms added to the sides of the columns and rows. Since the data is binary, the distances that are calculated among the columns and among the rows are computed with a binary distance function which is the asymmetric binary function. This method assumes that non zero elements are ON and zero elements are OFF. The distance is the proportion of bits in which only one is ON amongst those in which at least one is ON. Based on aligned sequences under study a heatmap is created that displays two way clustering of methylation status of all sequences and all aligned CpG positions.
聚类是一个类似功能的可视化和学习组的重要方法，也被广泛使用的芯片分析。在分析DNA甲基化数据集的情况下加以探讨矩阵是我* J二进制矩阵，我是克隆的序列和J是中央政府的立场。在这个矩阵中的每个索引有甲基化或为0的非甲基化CpG位点的价值1。质量检查的甲基化数据的基础上提供了一个层次聚类选项可以用在两个方面探讨CpG位点的甲基化（十）国家和探索克隆序列（一），甲基化状态分布的数据，在寻找聚类。非常重要，人们要记住，这种方法不考虑CpG位点的基因组排序。聚类方法，也可以是有用的，在质量控制检查。观察克隆PCR方法从同一产品在不同的聚类，可以指向质量差的克隆序列。在用于methVisual R包的聚类方法是热图（）从STAT包，这是一个添加行和列两侧的两个聚类的彩色图像功能。由于是二进制数据，计算各列和行间的距离是一个二进制的距离函数，它是不对称的二元函数的计算。此方法假定非零元素，则零个元素是关闭的。远处是位只有一个，其中至少有一个是ON之间的比例。正在研究序列的基础上创建1热图显示所有序列的甲基化状态的方式聚类和所有的CpG位置对齐。
值----------Value----------
Heat-Map image is displayed and optionally saved as postscript in given path and name.
热图的图像显示，并选择性地保存在给定的路径和名称的后记。
作者（S）----------Author(s)----------
Arie Zackay <arie.zackay@mail.huji.ac.il>,Christine Steinhoff <steinhof@molgen.mpg.de>
举例----------Examples----------
## using methData, file is the path to R home directory.[＃methData，文件是为R的主目录的路径。]
## In order to save heatMapMeth.pdf, make sure that you have writing [＃在为了节省heatMapMeth.pdf的，确保你写]
## permission under R.home() directory. If you do not have permission[＃许可根据R.home（目录）。如果你没有权限]
## choose your own path. [＃选择自己的道路。]
dir.create(file.path(R.home(component="home"),"/BiqAnalyzer"))
data(methData)
heatMapMeth(methData,file=file.path(R.home(component="home"),
"/BiqAnalyzer/heatMapMeth.pdf"))
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 00:43:23
