adjacency(WGCNA)
adjacency()所属R语言包：WGCNA
Calculate network adjacency
计算网络邻接
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Calculates (correlation or distance) network adjacency from given expression data or from a similarity.
网络邻接计算（相关性或距离）从给定的表达式的数据或从相似。
用法----------Usage----------
adjacency(datExpr, selectCols = NULL,
type = "unsigned", power = if (type=="distance") 1 else 6,
corFnc = "cor", corOptions = "use = 'p'",
distFnc = "dist", distOptions = "method = 'euclidean'")
adjacency.fromSimilarity(similarity, type = "unsigned", power = if (type=="distance") 1 else 6)
参数----------Arguments----------
参数：datExpr
data frame containing expression data. Columns correspond to genes and rows to samples.
数据框包含表达式的数据。列对应的样本的基因和行。
参数：similarity
a (signed) similarity matrix: square, symmetric matrix with entries between -1 and 1.
一个相似矩阵（签名）：正方形，对称矩阵的条目-1和1之间。
参数：selectCols
for correlation networks only (see below); can be used to select genes whose adjacencies will be calculated. Should be either a numeric vector giving the indices of the genes to be used, or a boolean vector indicating which genes are to be used.
相关网络（见下文），可以用来选择的基因，其邻接将被计算。应该是一个数值向量给要使用的基因的指数，或一个布尔矢量的指示要使用哪些基因。
参数：type
network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid", "distance".
网络类型。允许的值是（唯一的缩写）"unsigned"，"signed"，"signed hybrid"，"distance"。
参数：power
soft thresholding power.
软阈值功率。
参数：corFnc
character string specifying the function to be used to calculate co-expression similarity for correlation networks. Defaults to Pearson correlation. Any function returning values between -1 and 1 can be used.
字符串指定要使用的函数计算的相关网络的共表达相似。默认为Pearson相关。任何函数返回-1和1之间的值都可以使用。
参数：corOptions
character string specifying additional arguments to be passed to the function given by corFnc. Use "use = 'p', method = 'spearman'" to obtain Spearman correlation.
字符串指定额外的参数传递给函数的corFnc。使用"use = 'p', method = 'spearman'"获得Spearman等级相关。
参数：distFnc
character string specifying the function to be used to calculate co-expression similarity for distance networks. Defaults to the function dist. Any function returning non-negative values can be used.
指定的功能的字符串被用来计算用于远程网络的共表达相似。默认的功能dist。可用于任何函数返回非负值。
参数：distOptions
character string specifying additional arguments to be passed to the function given by distFnc. For example, when the function dist is used, the argument method can be used to specify various ways of computing the distance.
字符串指定额外的参数传递给函数的distFnc。例如，当功能dist用于参数method可以用于指定的距离的计算方法的各种方式。
Details
详细信息----------Details----------
The argument type determines whether a correlation (type one of "unsigned", "signed", "signed hybrid"), or a distance network (type equal "distance") will be calculated. In correlation networks the adajcency is constructed from correlations (values between -1 and 1, with high numbers meaning high similarity). In distance networks, the adjacency is constructed from distances (non-negative values, high values mean low similarity).
参数type判定的相关性（type1"unsigned"，"signed"，"signed hybrid"），或距离网络（type等于 "distance"）将被计算。在相关网络adajcency构造的相关性（-1到1之间的值，这意味着很高的相似性高的数字）。在远程网络，构建邻接的距离（非负值，高值意味着低的相似性）。
The function calculates the similarity of columns (genes) in datExpr by calling the function given in corFnc (for correlation networks) or distFnc (for distance networks), transforms the similarity according to type and raises it to power, resulting in a weighted network adjacency matrix. If selectCols is given, the corFnc function will be given arguments (datExpr, datExpr[selectCols], ...); hence the returned adjacency will have rows corresponding to all genes and columns corresponding to genes selected by selectCols.
该函数计算datExpr通过调用函数corFnc相关网络或distFnc（远程网络），将相似根据列的相似性（基因） type和提高到power，导致加权网络的邻接矩阵。 selectCols如果，corFnc功能将被给定的参数(datExpr, datExpr[selectCols], ...);因此，返回的的邻接将有行和列对应的基因选择selectCols所有的基因。
Correlation and distance are transformed as follows: for type = "unsigned", adjacency = |cor|^power; for type = "signed", adjacency = (0.5 * (1+cor) )^power; for type = "signed hybrid", adjacency = cor^power if cor>0 and 0 otherwise; and for type = "distance", adjacency = (1-(dist/max(dist))^2)^power.
相关和距离转化为type = "unsigned"，邻接= |肺心病| ^功率;type = "signed"，邻接=（0.5 *（1 + COR））^功率; type = "signed hybrid"如下：邻接= COR ^功率，如果相应的> 0，否则为0;type = "distance"，邻接=（1 - （区/最大（区））^ 2）^力量。
The function adjacency.fromSimilarity inputs a similarity matrix, that is it skips the correlation calculation step but is otherwise identical.
的功能adjacency.fromSimilarity输入的相似度矩阵，即它跳过的相关性计算步骤，但其他方面都相同。
值----------Value----------
Adjacency matrix of dimensions ncol(datExpr) times ncol(datExpr) (or the same dimensions as similarity). If selectCols was given, the number of columns will be the length (if numeric) or sum (if boolean) of selectCols.
邻接矩阵的维度ncol(datExpr)倍ncol(datExpr)（或相同的尺寸作为similarity）。如果selectCols给定的，将数列的长度（如数字）或SUM（如果是布尔值）的selectCols。
注意----------Note----------
When calculated from the datExpr, the network is always calculated among the columns of
当计算从的datExpr，网络总是计算各列之间的
（作者）----------Author(s)----------
Peter Langfelder and Steve Horvath
参考文献----------References----------
Network Analysis, Statistical Applications in Genetics and Molecular Biology, Vol. 4 No. 1, Article 17
modules. BMC Systems Biology 2007, 1:54
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。
|
发表于 2012-10-1 21:06:13
