preservationNetworkConnectivity(WGCNA)
preservationNetworkConnectivity()所属R语言包：WGCNA
Network preservation calculations
网络保全计算的
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function calculates several measures of gene network preservation. Given gene expression data in several individual data sets, it calculates the individual adjacency matrices, forms the preservation network and finally forms several summary measures of adjacency preservation for each node (gene) in the network.
此函数计算的基因网络保护的几个措施。鉴于几个个别的数据集的基因表达中的数据，计算个别的邻接矩阵，形成保护网络，并最终形成（基因）在网络中的每个节点的多个摘要的邻接保存措施。
用法----------Usage----------
preservationNetworkConnectivity(
multiExpr,
useSets = NULL, useGenes = NULL,
corFnc = "cor", corOptions = "use='p'",
networkType = "unsigned",
power = 6,
sampleLinks = NULL, nLinks = 5000,
blockSize = 1000,
setSeed = 12345,
weightPower = 2,
verbose = 2, indent = 0)
参数----------Arguments----------
参数：multiExpr
expression data in the multi-set format (see checkSets). A vector of lists, one per set. Each set must contain a component data that contains the expression data, with rows corresponding to samples and columns to genes or probes.
表达在多集的格式的数据（见checkSets）。一个向量的列表，每一个组。每个集必须包含一个组件data包含的表达数据，与对应的基因或探针的样品和列的行。
参数：useSets
optional specification of sets to be used for the preservation calculation. Defaults to using all sets.
可选规范的集被用于保存计算。默认使用所有集合。
参数：useGenes
optional specification of genes to be used for the preservation calculation. Defaults to all genes.
可选规范的基因被用于保存计算。默认为所有的基因。
参数：corFnc
character string containing the name of the function to calculate correlation. Suggested functions include "cor" and "bicor".
含有计算相关的函数名称的字符串。建议功能包括"cor"和"bicor"。
参数：corOptions
further argument to the correlation function.
进一步的相关函数的参数。
参数：networkType
a character string encoding network type. Recognized values are (unique abbreviations of) "unsigned", "signed", and "signed hybrid".
一个字符串编码的网络类型。可识别的值是（唯一的缩写）"unsigned"，"signed"和"signed hybrid"。
参数：power
soft thresholding power for network construction. Should be a number greater than 1.
软阈值功率的网络建设。应该是一个大于1的数字。
参数：sampleLinks
logical: should network connections be sampled (TRUE) or should all connections be used systematically (FALSE)?
符合逻辑的：网络连接取样（TRUE）的所有连接系统（FALSE）？
参数：nLinks
number of links to be sampled. Should be set such that nLinks * nNeighbors be several times larger than the number of genes.
以被采样的链接数。应设置，使得nLinks * nNeighbors基因的数目大于几次。
参数：blockSize
correlation calculations will be split into square blocks of this size, to prevent running out of memory for large gene sets.
相关计算将被分成这样大小的方块，以防止运行大型基因组的内存。
参数：setSeed
seed to be used for sampling, for repeatability. If a seed already exists, it is saved before the sampling starts and restored upon exit.
种子被用于采样，可重复性。如果种子已经存在，它被保存在采样开始前和恢复后退出。
参数：weightPower
power with which higher adjacencies will be weighted in weighted means
高功率邻接将加权加权平均值
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----------
The preservation network is formed from adjacencies of compared sets. For 'complete' preservations, all given sets are compared at once; for 'pairwise' preservations, the sets are compared in pairs. Unweighted preservations are simple mean preservations for each node; their weighted counterparts are weighted averages in which a preservation of adjacencies A[i,j; 1] and A[i,j; 2] of nodes i,j between sets 1 and 2 is weighted by ( (A[i,j; 1]+A[i,j; 2])/2)^weightPower. The hyperbolic preservation is based on tanh[( max - min)/(max+min)^2], where max and min are the componentwise maximum and minimum of the compared adjacencies, respectively.
从邻接的比较组的保存网络形成。 “完整的”保留地，所有给定一次相比，配对保鲜剂，集成对比较。未加权的保鲜剂是简单的保鲜剂的每个节点，其加权平均的加权平均数，其中保存邻接A[i,j; 1]和A[i,j; 2]节点i,j集1和2之间的加权 X>。双曲保全措施的基础上， ( (A[i,j; 1]+A[i,j; 2])/2)^weightPower，其中tanh[( max - min)/(max+min)^2]和max是比较相邻的分支最大和最小的分别。
值----------Value----------
A list with the following components:
以下组件列表：
参数：pairwise
a matrix with rows corresponding to genes and columns to unique pairs of given sets, giving the pairwise preservation of the adjacencies connecting the gene to all other genes.
与基因和独特的对给定集的列对应的行的矩阵，使成对的保存的邻接的基因连接到所有其他的基因。
参数：complete
a vector with one entry for each input gene containing the complete mean preservation of the adjacencies connecting the gene to all other genes.
用一个条目为每个输入基因含有完整的平均保存的邻接的基因连接到所有其他的基因的向量。
参数：pairwiseWeighted
a matrix with rows corresponding to genes and columns to unique pairs of given sets, giving the pairwise weighted preservation of the adjacencies connecting the gene to all other genes.
与基因和独特的对给定集的列对应的行的矩阵，使成对的加权保存的邻接的基因连接到所有其他的基因。
参数：completeWeighted
a vector with one entry for each input gene containing the complete weighted mean preservation of the adjacencies connecting the gene to all other genes.
用一个条目为每个输入含有保存的邻接的基因连接到所有其他的基因的完整的加权均值基因的向量。
参数：pairwiseHyperbolic
a matrix with rows corresponding to genes and columns to unique pairs of given sets, giving the pairwise hyperbolic preservation of the adjacencies connecting the gene to all other genes.
与基因和独特的对给定集的列对应的行的矩阵，使成对的双曲保存的邻接的基因连接到所有其他的基因。
参数：completeHyperbolic
a vector with one entry for each input gene containing the complete mean hyperbolic preservation of the adjacencies connecting the gene to all other genes.
一个条目为每个输入包含完整的基因的向量与平均双曲线保存的邻接的基因连接到所有其他的基因。
参数：pairwiseWeightedHyperbolic
a matrix with rows corresponding to genes and columns to unique pairs of given sets, giving the pairwise weighted hyperbolic preservation of the adjacencies connecting the gene to all other genes.
与基因和独特的对给定集的列对应的行的矩阵，使成对的加权双曲保存的邻接的基因连接到所有其他的基因。
参数：completeWeightedHyperbolic
a vector with one entry for each input gene containing the complete weighted hyperbolic mean preservation of the adjacencies connecting the gene to all other genes.
用一个条目为每个输入含有完整的加权双曲平均保存的邻接的基因连接到所有其他的基因的基因的向量。
（作者）----------Author(s)----------
Peter Langfelder
参考文献----------References----------
参见----------See Also----------
adjacency for calculation of adjacency;
adjacency邻接计算;
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 2012-10-1 21:30:59
