ISA(eisa)
ISA()所属R语言包：eisa
Iterative Signature Algorithm on Gene Expression data
基因表达数据的迭代签名算法
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Run ISA on an ExpressionSet with the default parameters.
运行在默认参数ExpressionSet ISA。
用法----------Usage----------
ISA (data, flist = filterfun(function(x) IQR(x) > 0.5),
uniqueEntrez = TRUE, thr.gene = seq(2, 4, by = 0.5),
thr.cond = seq(1, 3, by = 0.5), no.seeds = 100)
参数----------Arguments----------
参数：data
The input, an ExpressionSet object.
输入，ExpressionSet的对象。
参数：flist
A "list" of filter functions to apply to the array. This is passed to the genefilter function without touching it. Supply NA here if you don't want to filter the expression set before running ISA on it.
A“名单”过滤功能，适用于阵列。这是通过genefilter函数，而不触及它。供应NA在这里，如果你不想过滤器之前，运行ISA它的设置表达。
参数：uniqueEntrez
Logical scalar, whether to filter the input expression set to keep exactly one probeset for each Entrez gene. Probesets that are not mapped to an Entrez gene are dropped.
逻辑标量，是否设置保持为每个Entrez基因只有一个probeset筛选输入表达式。未映射到Entrez基因probesets被丢弃。
参数：thr.gene
Numeric vector. The threshold parameters for the ISA, for features (=probesets or genes). All combinations of thr.gene and thr.cond will be used to run ISA.
数字向量。为ISA的阈值参数，功能（= probesets或基因）。 thr.gene和thr.cond将用于运行ISA的所有组合。
参数：thr.cond
Numeric vector. The threshold parameters for the ISA, for samples. All combinations of thr.gene and thr.cond will be used to run ISA.
数字向量。为ISA的阈值参数，样品。 thr.gene和thr.cond将用于运行ISA的所有组合。
参数：no.seeds
Number of seeds to run ISA from.
运行ISA种子数量。
Details
详情----------Details----------
Please read tutorial vignette included in this package for an introduction on ISA. The isa2-package manual page in the isa2 package is also useful.
请仔细阅读教程暗角包括在此介绍了在ISA包。 isa2-packageisa2包的手册页也是有益的。
The ISA function performs the ISA algorithm on the supplied expression data. This involves the following steps:
ISA函数执行上所提供的基因表达数据的ISA算法。这包括以下步骤：
Filtering the features (i.e. probe sets) according to their variance. You will need the genefilter package for this. The default filtering function keeps the features that have an IQR of 0.5 or more. See genefilter for details on how to create filtering functions. If NA is given as the flist argument, then no filtering is performed.
过滤功能（即探针组），根据其方差。为此，你需要genefilter包。默认的过滤功能，保持功能IQR 0.5或以上。看到genefilter如何创建过滤功能的详细信息。如果NA作为flist参数，然后不执行筛选。
Filtering the features by mapping them to Entrez genes. Features that do not map to Entrez genes are removed from the data set. If more features map to the same Entrez gene, then only the one with the highest variance will be kept.
将它们映射到Entrez的基因筛选的功能。从数据集映射到Entrez的基因的功能，不被删除。如果有更多的功能映射到相同的Entrez基因，然后只用方差最高将被保留。
Calling the isa function in the isa2 package to perform the Iterative Signature Algorithm. This itself performs the following steps:
调用在isa包isa2函数来执行迭代签名算法。这本身执行以下步骤：
Normalizing the data by calling isa.normalize.
标准化数据调用isa.normalize。
Generating random input seeds via generate.seeds.
通过generate.seeds生成随机输入的种子。
Running ISA with all combinations of given feature and sample thresholds, by calling isa.iterate.
运行ISA功能和样品阈值的所有组合，通过调用isa.iterate。
Merging similar modules, separately for each threshold combination, by calling isa.unique.
合并类似的模块，分别为每个阈值相结合，通过调用isa.unique。
Filtering the modules separately for each threshold combination, by calling isa.filter.robust in the isa2 package.
过滤模块，分别为每个阈值相结合，通过调用isa.filter.robustisa2包。
Putting all modules from the runs with different thresholds into a single object.
从运行的所有模块到一个单一的对象放在不同的阈值。
Merging similar modules, across all threshold combinations, if two modules are similar, then the one with the milder thresholds is kept.
合并类似的模块，所有阈值的组合，如果两个模块都差不多，然后保持一个温和的阈值。
Creates an ISAModules object from the ISA results.
从ISA的结果创建一个ISAModules对象。
值----------Value----------
An ISAModules-class object.
ISAModules-class对象。
作者（S）----------Author(s)----------
Gabor Csardi <a href="mailto:Gabor.Csardi@unil.ch">Gabor.Csardi@unil.ch</a>
参考文献----------References----------
analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.
Revealing modular organization in the yeast transcriptional network Nat Genet. 2002 Aug;31(4):370-7. Epub 2002 Jul 22
Defining transcription modules using large-scale gene expression data Bioinformatics 2004 Sep 1;20(13):1993-2003. Epub 2004 Mar 25.
参见----------See Also----------
The vignette included in the eisa package.
eisa包中包含的小品文。
举例----------Examples----------
library(ALL)
data(ALL)
modules <- ISA(ALL, thr.gene=2.7, thr.cond=1.4)
modules
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 17:13:11
