mosaics-package(mosaics)
mosaics-package()所属R语言包：mosaics
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
马赛克（基于模型和两个样品芯片序列分析和推理）
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This package provides functions for fitting MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data.
这个软件包提供装修马赛克功能，统计分析样本框架或两样本的ChIP-seq的数据。
Details
详情----------Details----------
This package contains three main classes, BinData, MosaicsFit, and MosaicsPeak, which represent bin-level ChIP-seq data, MOSAiCS model fit, and MOSAiCS peak calling results, respectively. This package contains three main methods,readBins, mosaicsFit, and mosaicsPeak. constructBins method constructs bin-level files from the aligned read file. readBins method imports bin-level data and construct BinData class object. mosaicsFit method fits MOSAiCS model using BinData class object and constructs MosaicsFit class object. mosaicsPeak method calls peaks using MosaicsFit class object and construct MosaicsPeak class object. MosaicsPeak class object can be exported as text files or transformed into data frame and can be used for the downstream analysis. This package also provides methods for simple exploratory analysis.
这个软件包包含三大类，BinData，MosaicsFit，MosaicsPeak，这代表斌级芯片SEQ数据，马赛克模型拟合，马赛克高峰调用结果，分别。这个软件包包含三个主要的方法，readBins，mosaicsFit，mosaicsPeak。 constructBins方法构造斌级文件对齐的读文件。 readBins方法进口斌级数据和构造BinData类对象。 mosaicsFit方法适合使用BinData类对象的马赛克模型和构造MosaicsFit类的对象。 mosaicsPeak方法调用峰使用MosaicsFit类的对象和构造MosaicsPeak类的对象。 MosaicsPeak类对象可以导出为文本文件，或转化成数据框，并可以用于下游分析。这个包还提供了简单的探索性分析的方法。
The mosaics package companion website, http://www.stat.wisc.edu/~keles/Software/mosaics/, provides preprocessing scripts, preprocessed files for diverse reference genomes, and easy-to-follow instructions. We encourage questions or requests regarding mosaics package to be posted on our Google group, http://groups.google.com/group/mosaics_user_group. Please check the vignette for further details on the mosaics package and these websites.
http://www.stat.wisc.edu/~keles /软件/马赛克/mosaics包同伴网站提供预处理脚本，为不同的参考基因组的预处理文件，并易于遵循的指示。我们鼓励mosaics包被张贴在我们的Google组，http://groups.google.com/group/mosaics_user_group的问题或要求。请mosaics包和这些网站上的进一步细节的小插曲。
作者（S）----------Author(s)----------
Dongjun Chung, Pei Fen Kuan, Sunduz Keles
Maintainer: Dongjun Chung <chungdon@stat.wisc.edu>
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----------
constructBins, readBins, mosaicsFit, mosaicsPeak , BinData, MosaicsFit, MosaicsPeak.
constructBins，readBins，mosaicsFit，mosaicsPeak，BinData，MosaicsFit，MosaicsPeak。
举例----------Examples----------
## Not run: [＃无法运行：]
library(mosaicsExample)
exampleBinData <- readBins( type=c("chip","input","M","GC","N"),
fileName=c( system.file("extdata/chip_chr21.txt", package="mosaicsExample"),
system.file("extdata/input_chr21.txt", package="mosaicsExample"),
system.file("extdata/M_chr21.txt", package="mosaicsExample"),
system.file("extdata/GC_chr21.txt", package="mosaicsExample"),
system.file("extdata/N_chr21.txt", package="mosaicsExample") ) )
exampleBinData
print(exampleBinData)[1:10, ]
plot(exampleBinData)
plot( exampleBinData, plotType="M" )
plot( exampleBinData, plotType="GC" )
plot( exampleBinData, plotType="input" )
plot( exampleBinData, plotType="M|input" )
plot( exampleBinData, plotType="GC|input" )
exampleFit <- mosaicsFit( exampleBinData, analysisType="TS" )
exampleFit
plot(exampleFit)
estimates(exampleFit)
examplePeak <- mosaicsPeak( exampleFit, signalModel = "2S", FDR = 0.05 )
examplePeak
print(examplePeak)[1:10, ]
export( examplePeak, type = "txt", fileLoc = "./", fileName = "TSpeakList.txt" )
export( examplePeak, type = "bed", fileLoc = "./", fileName = "TSpeakList.bed" )
export( examplePeak, type = "gff", fileLoc = "./", fileName = "TSpeakList.gff" )
## 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。
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 01:07:47
