Cooccurrence(methVisual)
Cooccurrence()所属R语言包：methVisual
Visualization of binary methylation data
二进制的甲基化数据可视化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Visualization of binary methylation data including neighboured cooccurrence
二进制的甲基化数据包括neighboured共生的可视化
用法----------Usage----------
Cooccurrence(methData,file,real,lolli)
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
String; path and file name for saving the result. Default format is .pdf
字符串;路径和文件名，保存结果。默认格式为。PDF
参数：real
logical; real position (real=TRUE) or relative position (real=FLASE) according to the reference sequence
逻辑;实际位置（实际= TRUE），或根据参考序列的相对位置（实际= FLASE）
参数：lolli
Integer; size of lollipops
整数;大小的棒棒糖
Details
详情----------Details----------
Visualization of methylation states using lollipop graphs, percentage of methylation across experiments and value of neighboured cooccurrence due to calculation of spearman correlation. Every single CpG site is marked with a circle with the following characteristic, a filled circle represents a methylated CpG and an empty circle a non methylated one. The modification in methVisual lollipop plot is the calculation and visualization of dependencies (also known as cooccurrence) between neighbored methylated CpG site and non methylated CpG site. That means, given a set of bisulfite sequenced clones one would like to detect subgroups where specific CpG sites always occur coordinately either methylated or non methylated.
使用的棒棒糖图表，整个实验的甲基化比例和价值的neighboured共生由于计算Spearman相关的甲基化状态的可视化。每一个CpG位点的标记具有以下特点的圆，实心圆代表一个甲基化的CpG和非甲基化的一个空圈。修改在methVisual棒棒糖图是接壤的甲基化的CpG位点和非甲基化CpG位点之间的依赖的计算和可视化（也称为共生）。这意味着，一套一想检测亚特定CpG位点总是出现协调或者甲基化或非甲基硫酸氢钠测序克隆。
值----------Value----------
summary plot that will be saved by default as pdf file under the given path and name
总结图将被保存为PDF文件默认情况下，根据给定的路径和名称
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 Cooccurrence.pdf, make sure that you have writing [＃在为了节省Cooccurrence.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")) [dir.create（file.path组件（R.home（=“家”），“/ BiqAnalyzer”））]
data(methData)
Cooccurrence(methData,file=paste(tempdir(),"/Cooccurrence.pdf",sep=""))
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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
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 2012-2-26 00:43:05
