mosaicsPeak(mosaics)
mosaicsPeak()所属R语言包：mosaics
Call peaks based on fitted MOSAiCS model
呼叫装马赛克模型的基础上峰
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Call peaks using MosaicsFit class object, which is a fitted MOSAiCS model.
致电峰MosaicsFit类的对象，这是一个模型拟合马赛克。
用法----------Usage----------
mosaicsPeak( object, ... )
## S4 method for signature 'MosaicsFit'
mosaicsPeak( object, signalModel="2S", FDR=0.05, maxgap=200, minsize=50, thres=10 )
参数----------Arguments----------
参数：object
Object of class MosaicsFit, a fitted MOSAiCS model obtained using function mosaicsFit.
对象类MosaicsFit，模型拟合马赛克获得使用功能mosaicsFit。
参数：signalModel
Signal model. Possible values are "1S" (one-signal-component model) and "2S" (two-signal-component model). Default is "2S".
信号模型。可能的值是“1”（一个信号组件模型）和“2S”（两个信号组件模型）。默认是“2S”。
参数：FDR
False discovery rate. Default is 0.05.
虚假的发现率。默认值是0.05。
参数：maxgap
Initial nearby peaks are merged if the distance (in bp) between them is less than maxgap. Default is 200.
初步附近的峰合并，如果它们之间的距离（BP）是比maxgap少。默认是200。
参数：minsize
An initial peak is removed if its width is narrower than minsize. Default is 50.
如果其宽度窄，比minsize初始峰被删除。默认值是50。
参数：thres
A bin within initial peak is removed if its ChIP tag counts are less than thres. Default is 10.
初始峰值内的垃圾桶被删除，如果其芯片的标记计数比thres少。默认值为10。
参数：...
Other parameters to be passed through to generic mosaicsPeak.
其他参数可以通过通用的mosaicsPeak。
Details
详情----------Details----------
When peaks are called, proper signal model needs to be specified. The optimal choice of the number of signal components depends on the characteristics of ChIP-seq data. In order to support users in the choice of optimal signal model, Bayesian Information Criterion (BIC) values and Goodness of Fit (GOF) plot are provided. BIC values and GOF plot can be obtained by applying show and plot methods to the MosaicsFit class object, which is a fitted MOSAiCS model. maxgap, minsize, and thres are for refining initial peaks called using specified signalModel and FDR.
被称为峰时，需要指定适当的信号模型。信号元件数量的最佳选择取决于对SEQ芯片数据的特点。为了支持用户在选择最佳的信号模型，贝叶斯信息标准（BIC）值和拟合优度（GOF）来积。可以通过申请show和plot方法MosaicsFit类的对象，这是一个模型拟合马赛克的BIC值和GOF的图。 maxgap，minsize，thres被称为精炼初始峰使用指定signalModel和FDR。
If you use a bin size shorter than the average fragment length of the experiment, set maxgap to the average fragment length and minsize to the bin size. If you set the bin size to the average fragment length or if bin size is larger than the average fragment length, set maxgap to the average fragment length and minsize to a value smaller than the average fragment length. See the vignette for further details.
如果你使用一个bin的大小设置maxgap片段的平均长度和minsize到bin大小，比实验的平均片段长度较短。如果您设置的bin大小平均片段长度或BIN大小是比一般的片段长度，设置maxgap片段的平均长度和minsize一个值小于平均片段长度较大。看到进一步的细节的小插曲。
值----------Value----------
Construct MosaicsPeak class object.
构建MosaicsPeak类的对象。
作者（S）----------Author(s)----------
Dongjun Chung, Pei Fen Kuan, Sunduz Keles
参考文献----------References----------
"A Statistical Framework for the Analysis of ChIP-Seq Data", Journal of the American Statistical Association, Vol. 106, pp. 891-903.
参见----------See Also----------
mosaicsFit , MosaicsPeak, MosaicsFit.
mosaicsFit，MosaicsPeak，MosaicsFit。
举例----------Examples----------
## Not run: [＃无法运行：]
library(mosaicsExample)
data(exampleFit)
examplePeak <- mosaicsPeak( exampleFit, signalModel = "2S", FDR = 0.05 )
## End(Not run)[＃结束（不运行）]
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 01:08:15
