HTSanalyzeR-package(HTSanalyzeR)
HTSanalyzeR-package()所属R语言包：HTSanalyzeR
HTSanalyzeR Package Overview
HTSanalyzeR包装概述
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. The over- representation analysis is performed based on hypergeometric tests. The enrichment analysis is based on the GSEA algorithm (Subramanian et al. PNAS 2005). The network analysis identifies enriched subnetworks based on algorithms from the BioNet package (Beisser et al., Bioinformatics 2010). A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package.
这个包提供了类和基因组表示，丰富和网络分析，高通量筛选方法。过度代表性的分析是基于超几何试验。富集分析的基础上的的GSEA算法（Subramanian等人。国家科学院院刊2005年）。网络分析，确定了从生物网包（Beisser等2010），生物信息学算法基于丰富的子网。管道还专门为cellHTS2对象执行综合网络分析，高通量RNA干扰屏幕。用户可以建立自己的分析管道，这个包的基础上设置自己的数据。
Details
详情----------Details----------
The most important classes in this package are 'GSCA' (Gene Set Collection Analyses) and 'NWA' (NetWork Analyses). As an example, a pipeline (see function 'HTSanalyzeR4cellHTS2') is developed in this package for cellHTS2 screen analyses. Based on these two classes and other functions, users can design their own pipelines specifically for their own data sets.
在此包中最重要的类是GSCA“（基因组收集分析）和”西北航空“（网络分析）。管道（见函数HTSanalyzeR4cellHTS2“）作为一个例子，在这一揽子为cellHTS2屏幕分析。基于这两个类和其他功能，用户可以设计自己的管道，专门为自己的数据集。
Full help on classes and associated functions is available from within class help pages.
类和相关职能的充分的帮助是从内部类的帮助页。
Introductory information on the use of classes and pipeline are available in the vignette, typeopenVignette().
使用类和管道上的介绍资料中的小插曲，类型openVignette()。
A full listing of documented topics is available in HTML view by typing help.start() and selecting the HTSanalyzeR package from the Packages menu or via library(help="HTSanalyzeR").
键入help.start()和选择HTSanalyzeR菜单或通过Packages的library(help="HTSanalyzeR")包的记录主题的完整列表可在HTML视图。
作者（S）----------Author(s)----------
Xin Wang, Camille D.A. Terfve, John C. Rose, and Florian Markowetz
Maintainer: Xin Wang <Xin.Wang@cancer.org.uk>
参考文献----------References----------
Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.
for the functional analysis of biological networks. Bioinformatics. 2010 Apr 15;26(8):1129-30.
functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008 24(13):i223-i231.
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 2012-2-25 21:56:08
