OrderEV(ExpressionView)
OrderEV()所属R语言包：ExpressionView
Find the optimal arrangement of biclusters for visualization in
寻找最佳安排用于可视化的biclusters
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Finds the optimal arrangement of possibly overlapping biclusters that maximizes the areas of the largest contiguous parts of the biclusters. The reordering is necessary to obtain a visually
发现可能重叠biclusters的最佳安排，最大限度地提高最大连续的biclusters的部分区域。获得视觉的重新安排是必要的
用法----------Usage----------
## S4 method for signature 'ISAModules'
OrderEV(biclusters, initialorder, maxtime, debuglevel)
## S4 method for signature 'Biclust'
OrderEV(biclusters, initialorder, maxtime, debuglevel)
## S4 method for signature 'list'
OrderEV(biclusters, initialorder, maxtime, debuglevel)
参数----------Arguments----------
参数：biclusters
An ISAModules object, a Biclust object or a named list. The last one is probably coming from the isa2 package.
ISAModules对象，Biclust对象或命名列表。最后一个可能是来自isa2包。
参数：initialorder
A list containing the initial order. Usually the output of a previous ordering.
一个列表，其中包含的初始订单。通常情况下，前一顺序的输出。
参数：maxtime
The maximal computation time in seconds. The default value is one minute (maxtime=60).
在几秒钟内最大的计算时间。默认值是一分钟（maxtime=60）。
参数：debuglevel
The level of information provided during the ordering. By default, the debug output is turned off (debuglevel=0).
在订购提供的信息化水平。默认情况下，调试输出被关闭（debuglevel=0）。
Details
详情----------Details----------
OrderEV performs a brute-force ordering of the biclusters, treating the rows and the columns of the matrix independently. The ordering algorithm is described in more detail in the accompanying vignette of the package.
OrderEV执行的biclusters的的蛮力顺序，治疗的行和列矩阵的独立。排序算法更详细地描述在包随附的小插曲。
值----------Value----------
A named list is returned with the following elements:
命名列表返回以下内容：
参数：rows / genes
A list containing the maps between the rows of the initial and the optimally ordered gene expression matrix. The first element represents the map of the complete data set, while the subsequent entries contain the row maps of the data sets projected onto the individual clusters. This entry is called "rows" if the function is called with a simple list as the first argument, and "genes" otherwise.
一个列表，其中包含的初始行和优化有序的基因表达矩阵之间的图。第一个元素代表了完整的数据集的图，而随后的条目包含预计到各个聚类的数据集的行图。这个项目被称为rows一个简单的列表作为第一个参数，如果该功能被称为genes否则。
参数：cols / samples
A list containing the maps between the columns of the initial and the optimally ordered gene expression matrix. The first element represents the map of the complete data set, while the subsequent entries contain the column maps of the data sets projected onto the individual clusters. This entry is called "cols" if the function is called with a simple list as the first argument, and "samples" otherwise.
一个列表，其中包含初始列和优化有序的基因表达矩阵之间的图。第一个元素代表了完整的数据集的图，而随后的条目包含预计到各个聚类的数据集的列映射。这个项目被称为cols一个简单的列表作为第一个参数，如果该功能被称为samples否则。
参数：status
A list containing the status of the ordering. The list has two entries, named genes and samples (or rows and cols if the function was called with a simple list as the first argument). Each entry is a numeric vector of ones and zeros. A 1 indicates that the map is fully optimized, whereas a 0 signals that the ordering could not be completely within the given time frame.
一个列表，其中包含的排序状态。列表中有两个项目，命名为genes和samples（或rows和cols如果该函数被称为作为第一个参数的简单列表）。每个条目是一个数字1和0的向量。一个1表示，全面优化图，而0信号的顺序可能不完全是在给定的时间框架。
作者（S）----------Author(s)----------
Andreas L黶cher
<a href="mailto:andreas.luescher@a3.epfl.ch">andreas.luescher@a3.epfl.ch</a>
参见----------See Also----------
ExportEV, LaunchEV,
ExportEV，LaunchEV
举例----------Examples----------
## We generate some noisy in-silico data with biclusters,[＃我们产生一些与biclusters嘈杂的硅片数据，]
## scramble the initially ordered arrangement[＃争相初步有序排列]
## identify the bicluster with the Iterative Signature Algorithm (ISA)[＃bicluster确定迭代签名算法（ISA）]
## and order the results with the OrderEV function[＃并责令与OrderEV功能的结果]
library(isa2)
data.in.silico <- isa.in.silico(noise=0.1)[[1]]
data.in.silico <- data.in.silico[sample(c(1:dim(data.in.silico)[1])),
sample(c(1:dim(data.in.silico)[2]))]
isa.results <- isa(data.in.silico)
optimalorder <- OrderEV(isa.results)
str(optimalorder)
## Create a plot for the scrambled and the optimal orderings[＃创建一个杂乱的图和最优排序]
## Not run: [＃无法运行：]
layout(rbind(1:2))
image(data.in.silico)
image(data.in.silico[optimalorder$rows[[1]],
optimalorder$cols[[1]]])
## 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 2012-2-25 17:24:09
