trigger.net-methods(trigger)
trigger.net-methods()所属R语言包：trigger
Network-Trigger analysis
网络触发分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Network-Trigger analysis estimates the joint posterior probability of causal regulation for each pair of genes in the genome. These probabilities can further be used to construct a gene regulatory network.
触发网络分析估计，对每个基因在基因组中的因果关系调节的联合后验概率。这些概率可以进一步用来构建基因调控网络。
用法----------Usage----------
## S4 method for signature 'trigger'
trigger.net(triggerobj, gender = NULL, idx = NULL,
Bsec = 100, prob.cut = 0.7, include.loc = TRUE, seed = 123, inputfile = NULL)
参数----------Arguments----------
参数：triggerobj
An object of class trigger containing slot loc.obj with local-linkage probabilities and marker indices of the best local-linkage markers for genes in the genome. See trigger and trigger.loclink for details.
一个类的对象trigger包含插槽loc.obj与地方联动的概率和当地最好的联动在基因组的基因标记的标记指数。详情请参阅trigger和trigger.loclink。
参数：gender
Optional. When computing statistics involving markers on sex chromosome, gender of each sample should be specified.
可选的。当计算统计，涉及性染色体上的标记，gender每个样品应指定。
参数：idx
Optional. One can specify the indices of selected genes as putative regulators. By default, all the genes will be selected as putative regulators.
可选的。一个可以指定假定监管机构选定的基因指标。默认情况下，所有的基因将被选中作为假定的监管。
参数：Bsec
Number of iterations to perform when estimating null statistics for secondary-linkage and conditional independence.
迭代次数估计为二级联动和有条件的独立的空统计时执行。
参数：prob.cut
Probability threshold. The joint regulatory probabilities of a regulator to all the other genes will be set to zero if the local-linkage probability of the regulator is below the threshold; default prob.cut = 0.7.
概率阈值。将设置为零的所有其他基因的调节联合监管的概率，如果稳压器的本地联动的概率低于阈值;默认的prob.cut = 0.7。
参数：include.loc
Logical. If TRUE, the estimated posterior probability of regulation is more conservative.
逻辑。如果TRUE，调控后验概率的估计较为保守。
参数：seed
Optional. A numeric seed for reproducible results.
可选的。一个数字的种子可重复性的结果。
参数：inputfile
Optional. If provided, reads in the probability matrix from working directory.
可选的。如果提供，内容从工作目录中的概率矩阵。
Details
详情----------Details----------
The option idx contains the indices of putative regulator genes. When the data set is large, one can use this option by selecting a subset of genes as putative regulators in one computation and parallel-computes the genome-wide regulatory probability. If idx=NULL, all the genes will be computed for probability of regulation to other genes in the data.
选项idx包含假定的调节基因的指数。大数据集时，可以使用此选项中选择一个计算假定监管的基因子集和并行计算的全基因组的监管概率。 idx=NULL如果，所有的基因将数据中的其他基因调控的概率计算。
If include.loc = TRUE, the joint posterior probability of regulation is the product of local-linkage, secondary-linkage and conditional independence. Otherwise, it is the product of secondary-linkage and conditional independence. The local-linkage is not a necessary condition for calculating regulation probability. If the probability of local-linkage is considered, the joint probability of regulation is more conservative. See references for details.
如果include.loc = TRUE，监管的联合后验概率是地方联动，二级联动和条件的独立的产品。否则，它是独立二级联动和条件的产品。本地联动不是调控的概率计算的一个必要条件。如果本地联动的概率被认为，监管的联合概率是比较保守。有关详情，请参阅参考。
值----------Value----------
A matrix of genome-wide regulatory probabilities with putative regulators in rows and regulated genes in columns. Note that the matrix is not symmetric. If gene i is estimated to be causal for gene j with high probability, the reverse is not true.
一个矩阵的行和列的调节基因的全基因组假定监管机构的监管与概率。请注意，不是对称矩阵。如果基因，我估计是基因j的概率很高的因果，反之则不然。
作者（S）----------Author(s)----------
Lin S. Chen <a href="mailto:lschen.stat@gmail.com">lschen.stat@gmail.com</a>, Dipen P. Sangurdekar <a href="mailto:dps@genomics.princeton.edu">dps@genomics.princeton.edu</a> and John D. Storey <a href="mailto:jstorey@princeton.edu">jstorey@princeton.edu</a>
参考文献----------References----------
参见----------See Also----------
trigger.loclink, trigger.netPlot2ps and trigger.trait
trigger.loclink，trigger.netPlot2ps和trigger.trait
举例----------Examples----------
## Not run: [＃无法运行：]
data(yeast)
attach(yeast)
triggerobj <- trigger.build(marker = marker, exp = exp,
marker.pos = marker.pos, exp.pos = exp.pos)
triggerobj <- nettrig.loc(triggerobj, window.size = 30000)
trig.prob <- trigger.net(triggerobj, Bsec = 100)
netPlot2ps(trig.prob)
detach(yeast)
## 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 15:46:01
