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[software] 用R包BayesPeak来对CHIP-seq数据call peaks

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发表于 2017-5-22 22:54:10 | 显示全部楼层 |阅读模式
首先当然是我们菜鸟团的博客链接啦
http://www.bio-info-trainee.com/1749.html

输入得是Bed格式的文件

其实最重要的就是这两个函数:
[AppleScript] 纯文本查看 复制代码
Bayespeak()
 ##performs the algorithm described above on a given experiment, consisting of
either one or two data sets - a treated data set must be supplied, which can optionally be complemented by
a control data set. Each of these data sets must be in .bed format, and can be specied as a le location,
a data.frame containing the columns \chr", \start", \end", \strand" (specied as forward, \+", or reverse, \-"),
or a RangedData object from theIRanges package in BioConductor.
summarize.peaks()  
## the function summarize.peaks will do : Filtering of unenriched jobs/Filtering of unenriched bins/Assembly of enriched bins/Conversion of bins to peaks


之后绘图pp的直方图来判断
High density of reads,:直方图覆盖整个横轴[0,1]
Low density of reads:直方图稀稀拉拉,有的地方有,有的地方没有
Overfi tting:可能只有正链或者负链的富集。有偏向性
  
之后是注释找到基因吧。

欢迎指出错误。之后发现错误也会过来自己改的




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