nearestNeighborConnectivityMS(WGCNA)
nearestNeighborConnectivityMS()所属R语言包：WGCNA
Connectivity to a constant number of nearest neighbors across multiple data sets
跨多个数据集的恒定数量的最近邻的连接
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Given expression data from several sets and basic network parameters, the function calculates connectivity of each gene to a given number of nearest neighbors in each set.
鉴于从几个集和基本网络参数的表达数据，该函数将计算每个基因的连接到每个集合中的给定数目的最近邻。
用法----------Usage----------
nearestNeighborConnectivityMS(multiExpr, nNeighbors = 50, power = 6,
type = "unsigned", corFnc = "cor", corOptions = "use = 'p'",
blockSize = 1000,
sampleLinks = NULL, nLinks = 5000, setSeed = 36492,
verbose = 1, indent = 0)
参数----------Arguments----------
参数：multiExpr
expression data in multi-set format. A vector of lists, one list per set. In each list there must be a component named data whose content is a matrix or dataframe or array of dimension 2 containing the expression data. Rows correspond to samples and columns to genes (probes).
多组表达数据的格式。一个向量的列表，一个列表，每一套。在每个列表中，必须有一个名为data，其内容是一个矩阵或数据框或阵列的尺寸2包含的表达数据的组件。行对应的基因样本和列（探针）。
参数：nNeighbors
number of nearest neighbors to use.
最近的邻居使用的数量。
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：type
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：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：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：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：setSeed
seed to be used for sampling, for repeatability. If a seed already exists, it is saved before the sampling starts and restored after.
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。
参数：verbose
integer controlling the level of verbosity. 0 means silent.
整数控制的详细程度。 0表示沉默。
参数：indent
integer controlling indentation of output. Each unit above 0 adds two spaces.
整数控制缩进输出。 0以上的每个单元增加了两个空格。
Details
详细信息----------Details----------
Connectivity of gene i is the sum of adjacency strengths between gene i and other genes; in this case we take the nNeighbors nodes with the highest connection strength to gene i. The adjacency strengths are calculated by correlating the given expression data using the function supplied in corFNC and transforming them into adjacency according to the given network type and power.
的基因i的连接是基因i和其他基因之间的邻接优势的总和，在这种情况下，我们采取的基因nNeighbors节点的连接强度最高的i的。邻接强度计算通过关联表达给定的数据使用在corFNC提供的功能和它们转化成邻接，根据给定的网络type和power。
值----------Value----------
A matrix in which columns correspond to sets and rows to genes; each entry contains the nearest neighbor connectivity of the corresponding gene.
A矩阵的列相对应的基因集和行，每个条目包含的最近邻连接的相应的基因。
（作者）----------Author(s)----------
Peter Langfelder
参见----------See Also----------
adjacency, softConnectivity,
adjacency，softConnectivity，
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 21:18:38
