vectorTOM(WGCNA)
vectorTOM()所属R语言包：WGCNA
Topological overlap for a subset of the whole set of genes
的整个基因组的一个子集的拓扑重叠
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function calculates topological overlap of a small set of vectors with respect to a whole data set.
此函数计算相对于整个数据集的一个小的矢量集的拓扑重叠。
用法----------Usage----------
vectorTOM(
datExpr,
vect,
subtract1 = FALSE,
blockSize = 2000,
corFnc = "cor", corOptions = "use = 'p'",
networkType = "unsigned",
power = 6,
verbose = 1, indent = 0)
参数----------Arguments----------
参数：datExpr
a data frame containing the expression data of the whole set, with rows corresponding to samples and columns to genes.
含有一整套的表达数据的一个数据框的行对应的样品和列的基因。
参数：vect
a single vector or a matrix-like object containing vectors whose topological overlap is to be calculated.
一个单一的矢量或矩阵状的对象，它包含向量，其拓扑重叠以计算。
参数：subtract1
logical: should calculation be corrected for self-correlation? Set this to TRUE if vect contains a subset of datExpr.
逻辑：应计算进行修正自相关？设置为TRUE如果vect包含的一个子集datExpr。
参数：blockSize
maximum block size for correlation calculations. Only important if vect contains a large number of columns.
最大块大小的相关性计算。只有重要的，如果vect包含了大量的列数。
参数：corFnc
character string giving the correlation function to be used for the adjacency calculation. Recommended choices are "cor" and "bicor", but other functions can be used as well.
字符字符串，给出要用于邻接计算的相关函数。推荐选择是"cor"和"bicor"，以及其他功能都可以使用。
参数：corOptions
character string giving further options to be passed to the correlation function.
提供进一步的相关函数的选项传递的字符串。
参数：networkType
character string giving network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid". See adjacency.
网络类型的字符串。允许的值是（）"unsigned"，"signed"，"signed hybrid"唯一的缩写。见adjacency。
参数：power
soft-thresholding power for network construction.
软阈值功率的网络建设。
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----------
Topological overlap can be viewed as the normalized count of shared neighbors encoded in an adjacency matrix. In this case, the adjacency matrix is calculated between the columns of vect and datExpr and the topological overlap of vectors in vect measures the number of shared neighbors in datExpr that vectors of vect share.
拓扑的重叠，可以被看作是归一计数共享邻接矩阵中编码的邻居。在这种情况下，计算的邻接矩阵vect和datExpr和vect测量的数目的共享邻居datExpr的向量的向量的拓扑重叠的列之间vect份额。
值----------Value----------
A matrix of dimensions n*n, where n is the number of columns in vect.
维度的矩阵n*n，其中n是在vect的列数。
（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----------
TOMsimilarity for standard calculation of topological overlap.
TOMsimilarity为标准计算的拓扑重叠。
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 22:25:45
