TOMsimilarity(WGCNA)
TOMsimilarity()所属R语言包：WGCNA
Topological overlap matrix similarity and dissimilarity
拓扑重叠矩阵的相似性和相异性
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Calculation of the topological overlap matrix from a given adjacency matrix.
从一个给定的邻接矩阵的拓扑重叠矩阵计算。
用法----------Usage----------
TOMsimilarity(adjMat, TOMType = "unsigned", TOMDenom = "min", verbose = 1, indent = 0)
TOMdist(adjMat, TOMType = "unsigned", TOMDenom = "min", verbose = 1, indent = 0)
参数----------Arguments----------
参数：adjMat
adjacency matrix, that is a square, symmetric matrix with entries between 0 and 1 (negative values are allowed if TOMType=="signed").
邻接矩阵，即0和1之间的条目是一个正方形，对称矩阵（负值被允许：如果TOMType=="signed"）。
参数：TOMType
a character string specifying TOM type to be calculated. One of "unsigned", "signed". If "unsigned", the standard TOM will be used (more generally, TOM function will receive the adjacency as input). If "signed", TOM will keep track of the sign of the adjacency between neighbors.
一个字符的字符串指定TOM类型来计算的。一个"unsigned"，"signed"。如果"unsigned"，标准的TOM将使用（更一般地，TOM函数将接收到作为输入的邻接）。如果"signed"，TOM将跟踪邻居的邻接关系的符号。
参数：TOMDenom
a character string specifying the TOM variant to be used. Recognized values are "min" giving the standard TOM described in Zhang and Horvath (2005), and "mean" in which the min function in the denominator is replaced by mean. The "mean" may produce better results but at this time should be considered experimental.
要使用的字符的字符串指定的TOM变种。公认的价值观是"min"的给标准TOM张和霍瓦特（2005年）中描述的，"mean"在其中min函数分母中的被替换的mean。 "mean"可能会产生更好的结果，但在这个时候，应考虑实验。
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 functions perform basically the same calculations of topological overlap. TOMdist turns the overlap (which is a measure of similarity) into a measure of dissimilarity by subtracting it from 1.
功能执行基本相同的拓扑重叠的计算。 TOMdist打开成衡量相异的重叠（这是一个相似性量度），通过从1中减去它。
Basic checks on the adjacency matrix are performed and missing entries are replaced by zeros. If TOMType = "unsigned", entries of the adjacency matrix are required to lie between 0 and 1; for TOMType = "signed" they can be between -1 and 1. In both cases the resulting TOM entries, as well as the corresponding dissimilarities, lie between 0 and 1.
的邻接矩阵进行基本检查和遗失的项目所取代零。如果TOMType = "unsigned"，的邻接矩阵的条目必须介于0和1;TOMType = "signed"它们可以是-1和1之间。在这两种情况下所得到的TOM条目，以及相应的不同点，在于在0和1之间。
The underlying C code assumes that the diagonal of the adjacency matrix equals 1. If this is not the case, the diagonal of the input is set to 1 before the calculation begins.
底层的C代码假定的邻接矩阵对角线等于1。如果这不是的情况下，对角线的输入被设置为1，在计算开始之前。
值----------Value----------
A matrix holding the topological overlap.
矩阵的拓扑重叠。
（作者）----------Author(s)----------
Peter Langfelder
参考文献----------References----------
Network Analysis", Statistical Applications in Genetics and Molecular Biology: Vol. 4: No. 1, Article 17
参见----------See Also----------
TOMsimilarityFromExpr
TOMsimilarityFromExpr
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 22:24:47
