simulateMultiExpr(WGCNA)
simulateMultiExpr()所属R语言包：WGCNA
Simulate multi-set expression data
模拟多组表达数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Simulation of expression data in several sets with relate module structure.
表达数据的多套与相关模拟模块结构。
用法----------Usage----------
simulateMultiExpr(eigengenes,
nGenes,
modProportions,
minCor = 0.5, maxCor = 1,
corPower = 1,
backgroundNoise = 0.1,
leaveOut = NULL,
signed = FALSE,
propNegativeCor = 0.3,
geneMeans = NULL,
nSubmoduleLayers = 0,
nScatteredModuleLayers = 0,
averageNGenesInSubmodule = 10,
averageExprInSubmodule = 0.2,
submoduleSpacing = 2,
verbose = 1, indent = 0)
参数----------Arguments----------
参数：eigengenes
the seed eigengenes for the simulated modules in a multi-set format. A list with one component per set. Each component is again a list that must contain a component data. This is a data frame of seed eigengenes for the corresponding data set. Columns correspond to modules, rows to samples. Number of samples in the simulated data is determined from the number of samples of the eigengenes.
的种子特征基因在一个多组的格式为模拟模块。一个列表，每个组的一个组成部分。每个组件又是一个列表，它必须包含一个组成部分data。这是一个数据框对应的数据集的种子特征基因。列对应的模块，行的样品。在模拟数据的样本数来确定的特征基因的样本的数量。
参数：nGenes
integer specifyin the number of simulated genes.
整数specifyin模拟基因的数目。
参数：modProportions
a numeric vector with length equal the number of eigengenes in eigengenes plus one, containing fractions of the total number of genes to be put into each of the modules and into the "grey module", which means genes not related to any of the modules. See details.
一个数值向量的长度等于在eigengenes加一，含有馏分被放入各模块并进入“灰色模块”，基因的总数，这意味着不相关的基因的特征基因的数目任何模块。查看详细信息。
参数：minCor
minimum correlation of module genes with the corresponding eigengene. See details.
模块的基因与相应的eigengene最小相关。查看详细信息。
参数：maxCor
maximum correlation of module genes with the corresponding eigengene. See details.
模块的基因与相应的eigengene最大相关。查看详细信息。
参数：corPower
controls the dropoff of gene-eigengene correlation. See details.
控制空投基因eigengene相关。查看详细信息。
参数：backgroundNoise
amount of background noise to be added to the simulated expression data.
背景噪声的量被添加到模拟的表达数据。
参数：leaveOut
optional specification of modules that should be left out of the simulation, that is their genes will be simulated as unrelated ("grey"). A logical matrix in which columns correspond to sets and rows to modules. Wherever TRUE, the corresponding module in the corresponding data set will not be simulated, that is its genes will be simulated independently of the eigengene.
可选的规格，应留出的模拟模块，这是他们的基因将模拟无关（“灰色”）。逻辑矩阵列对应的模块集和行。无论TRUE，对应的数据组中的对应模块不会被模拟，这是它的基因，将模拟的eigengene独立。
参数：signed
logical: should the genes be simulated as belonging to a signed network? If TRUE, all genes will be simulated to have positive correlation with the eigengene. If FALSE, a proportion given by propNegativeCor will be simulated with negative correlations of the same absolute values.
逻辑的基因签署的网络模拟？如果TRUE，所有基因将模拟的有正相关的eigengene的。如果FALSE，由propNegativeCor的比例将相同的绝对值呈负相关的模拟。
参数：propNegativeCor
proportion of genes to be simulated with negative gene-eigengene correlations. Only effective if signed is FALSE.
的基因的比例是模拟具有负的基因eigengene相关的。只有有效的，如果signed是FALSE。
参数：geneMeans
optional vector of length nGenes giving desired mean expression for each gene. If not given, the returned expression profiles will have mean zero.
可选的矢量的长度nGenes给需要的平均每个基因的表达。如果没有给出，返回的表达谱具有均值为零。
参数：nSubmoduleLayers
number of layers of ordered submodules to be added. See details.
要添加的层的排列的子模块的数量。查看详细信息。
参数：nScatteredModuleLayers
number of layers of scattered submodules to be added. See details.
要添加的层的散射子模块的数量。查看详细信息。
参数：averageNGenesInSubmodule
average number of genes in a submodule. See details.
平均数的基因中的一个子模块。查看详细信息。
参数：averageExprInSubmodule
average strength of submodule expression vectors.
子模块表达向量的平均强度。
参数：submoduleSpacing
a number giving submodule spacing: this multiple of the submodule size will lie between the submodule and the next one.
一些子模块间距：这多个子模块的尺寸将介于子模块下一个。
参数：verbose
integer level of verbosity. Zero means silent, higher values make the output progressively more and more verbose.
整数的详细程度。零表示沉默，较高的值使输出越来越多，更详细。
参数：indent
indentation for diagnostic messages. Zero means no indentation, each unit adds two spaces.
缩进诊断消息。零表示无压痕，每个单元增加两个空格。
Details
详细信息----------Details----------
For details of simulation of individual data sets and the meaning of individual set simulation arguments, see simulateDatExpr. This function simulates several data sets at a time and puts the result in a multi-set format. The number of genes is the same for all data sets. Module memberships are also the same, but modules can optionally be “dissolved”, that is their genes will be simulated as unassigned. Such “dissolved”, or left out, modules can be specified in the matrix leaveOut.
单个数据集的仿真，并个别集仿真参数的含义的详细信息，请参阅simulateDatExpr。此函数模拟几个数据集在一个时间，并将结果在多集的格式。基因的数量是相同的所有数据集。模块的成员是相同的，但模块可以选择“溶解”，这是他们的基因将被模拟为未分配。这样的“溶解”，或离开了，模块可以指定矩阵中的leaveOut。
值----------Value----------
A list with the following components:
以下组件列表：
参数：multiExpr
simulated expression data in multi-set format analogous to that of the input eigengenes. A list with one component per set. Each component is again a list that must contains a component data. This is a data frame of expression data for the corresponding data set. Columns correspond to genes, rows to samples.
模拟多设置的格式类似于输入eigengenes中的表达数据。一个列表，每个组的一个组成部分。每个组件又是一个列表，该列表必须包含一个组件data。表达为相应的数据集的数据，这是一个数据框。列对应的基因，行的样本。
参数：setLabels
a matrix of dimensions (number of genes) times (number of sets) that contains module labels for each genes in each simulated data set.
的矩阵尺寸（数目的基因）倍（套），它包含在每个模拟的数据集的每个基因的模块的标签。
参数：allLabels
a matrix of dimensions (number of genes) times (number of sets) that contains the module labels that would be simulated if no module were left out using leaveOut. This means that all columns of the matrix are equal; the columns are repeated for convenience so allLabels has the same dimensions as setLabels.
的维度的矩阵（基因数）倍（套），其中包含的模块的标签，如果没有模块将模拟的留在外面使用leaveOut。这意味着，所有列的矩阵是相等的;列重复为方便起见，所以allLabelssetLabels具有相同的尺寸。
参数：labelOrder
a matrix of dimensions (number of modules) times (number of sets) that contains the order in which module labels were assigned to genes in each set. The first label is assigned to genes 1...(module size of module labeled by first label), the second label to the following batch of genes etc.
的矩阵尺寸（模块数）倍（套），它包含在哪个模块中的标签的顺序被分配给每个集合中的基因。被分配的第一个标签的基因1 ...（标记的第一个标签的模块的模块尺寸），所述第二标签的基因等的下面的批处理
（作者）----------Author(s)----------
Peter Langfelder
参考文献----------References----------
to the article
modules. BMC Systems Biology 2007, 1:54.
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/EigengeneNetwork/SupplementSimulations.pdf.
参见----------See Also----------
simulateEigengeneNetwork for a simulation of eigengenes with a given causal structure;
simulateEigengeneNetwork的模拟与给定的因果结构的特征基因;
simulateDatExpr for simulation of individual data sets;
simulateDatExpr模拟单个数据集;
simulateDatExpr5Modules for a simple simulation of a data set consisting of 5 modules;
simulateDatExpr5Modules数据集由5个模块组成的一个简单的模拟;
simulateModule for simulations of individual modules;
simulateModule各个模块的模拟;
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。
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发表于 2012-10-1 22:22:14
