pickSoftThreshold(WGCNA)
pickSoftThreshold()所属R语言包：WGCNA
Analysis of scale free topology for soft-thresholding
无标度拓扑结构的软阈值分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Analysis of scale free topology for multiple soft thresholding powers. The aim is to help the user pick an appropriate soft-thresholding power for network construction.
多处软阈值功率的无标度拓扑结构的分析。我们的目标是帮助用户选择一个合适的软阈值功率的网络建设。
用法----------Usage----------
pickSoftThreshold(
data,
dataIsExpr = TRUE,
RsquaredCut = 0.85,
powerVector = c(seq(1, 10, by = 1), seq(12, 20, by = 2)),
removeFirst = FALSE, nBreaks = 10, blockSize = 1000,
corFnc = "cor", corOptions = "use = 'p'",
networkType = "unsigned",
moreNetworkConcepts = FALSE,
verbose = 0, indent = 0)
pickSoftThreshold.fromSimilarity(
similarity,
RsquaredCut = 0.85,
powerVector = c(seq(1, 10, by = 1), seq(12, 20, by = 2)),
removeFirst = FALSE, nBreaks = 10, blockSize = 1000,
networkType = "unsigned",
moreNetworkConcepts=FALSE,
verbose = 0, indent = 0)
参数----------Arguments----------
参数：data
expression data in a matrix or data frame. Rows correspond to samples and columns to genes.
一个矩阵或数据框中的表达数据。行对应的样品和列的基因。
参数：dataIsExpr
logical: should the data be interpreted as expression (or other numeric) data, or as a similarity matrix of network nodes?
逻辑：数据应该被解释为表达式（或其他数字）的数据，或作为网络节点的相似度矩阵？
参数：similarity
similarity matrix: a symmetric matrix with entries between -1 and 1 and unit diagonal.
相似性矩阵：-1和1之间和单元对角线对称矩阵的条目。
参数：RsquaredCut
desired minimum scale free topology fitting index R^2.
自由拓扑结构所需的最小规模拟合指数R^2。
参数：powerVector
a vector of soft thresholding powers for which the scale free topology fit indices are to be calculated.
软阈值功率的矢量的无标度拓扑结构拟合指数的计算。
参数：removeFirst
should the first bin be removed from the connectivity histogram?
应的第一bin被删除从连通直方图？
参数：nBreaks
number of bins in connectivity histograms
在连通直方图，箱数
参数：blockSize
block size into which the calculation of connectivity should be broken up. If R runs into memory problems, decrease this value.
块大小的连接到该计算应该被打破。如果R运行到内存问题，减小该值。
参数：corFnc
a character string giving the correlation function to be used in adjacency calculation.
一个字符串给邻接计算中要使用的相关函数。
参数：corOptions
further options to the correlation function specified in corFnc.
进一步的相关函数指定的corFnc的选项。
参数：networkType
network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid". See adjacency.
网络类型。允许的值是（）"unsigned"，"signed"，"signed hybrid"唯一的缩写。见adjacency。
参数：moreNetworkConcepts
logical: should additional network concepts be calculated? If TRUE, the function will calculate how the network density, the network heterogeneity, and the network centralization depend on the power. For the definition of these additional network concepts, see Horvath and Dong (2008). PloS Comp Biol.
逻辑：额外的网络概念应如何计算？如果TRUE，该函数将计算网络密度，网络异质性，网络集中依赖于电源。这些额外的网络概念的定义，请参见霍瓦特和董（2008年）。科学公共图书馆比较生物学。
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 function calculates weighted networks either by interpreting data directly as similarity, or first transforming it to similarity of the type specified by networkType. The weighted networks are obtained by raising the similarity to the powers given in powerVector. For each power the scale free topology fit index is calculated and returned along with other information on connectivity.
该函数计算加权网络解释：“data直接的相似性，或将其转化为相似的类型指定的networkType。加权网络，得到提高的相似性所赋予的权力在powerVector。对于每个电源，无标度拓扑结构拟合指数的计算和连接的其他信息一起返回。
值----------Value----------
A list with the following components:
以下组件列表：
参数：powerEstimate
estimate of an appropriate soft-thresholding power: the lowest power for which the scale free topology fit R^2 exceeds RsquaredCut. If R^2 is below RsquaredCut for all powers, NA is returned.
适当的软阈值功率：功耗最低的无标度拓扑结构适合R^2超过RsquaredCut，估计。如果R^2是下面的RsquaredCut一切权力，NA返回。
参数：fitIndices
a data frame containing the fit indices for scale free topology. The columns contain the soft-thresholding power, adjusted R^2 for the linear fit, the linear coefficient, adjusted R^2 for a more complicated fit models, mean connectivity, median connectivity and maximum connectivity. If input moreNetworkConcepts is TRUE, 3 additional columns containing network density, centralization, and heterogeneity.
一个数据框包含的无标度拓扑结构的拟合指数。列包含软阈值功率，调整R^2的线性拟合的线性相关系数，调整R^2对于更复杂的飞度车型，意味着连接，中间连接和最大的连接。如果输入moreNetworkConcepts TRUE，3个附加列，其中包含网络密度，集中化和异质性。
（作者）----------Author(s)----------
Steve Horvath and Peter Langfelder
参考文献----------References----------
Network Analysis", Statistical Applications in Genetics and Molecular Biology: Vol. 4: No. 1, Article 17
4(8): e1000117
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 21:20:59
