TOMsimilarityFromExpr(WGCNA)
TOMsimilarityFromExpr()所属R语言包：WGCNA
Topological overlap matrix
拓扑重叠矩阵
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Calculation of the topological overlap matrix from given expression data.
从给定的表达数据的拓扑重叠矩阵的计算。
用法----------Usage----------
TOMsimilarityFromExpr(
datExpr,
corType = "pearson",
networkType = "unsigned",
power = 6,
TOMType = "signed",
TOMDenom = "min",
maxPOutliers = 1,
quickCor = 0,
pearsonFallback = "individual",
cosineCorrelation = FALSE,
nThreads = 0,
verbose = 1, indent = 0)
参数----------Arguments----------
参数：datExpr
expression data. A data frame in which columns are genes and rows ar samples. NAs are allowed, but not too many.
表达数据。一个数据框的基因，在哪些列和行AR样本。来港定居是允许的，但不是太多。
参数：corType
character string specifying the correlation to be used. Allowed values are (unique abbreviations of) "pearson" and "bicor", corresponding to Pearson and bidweight midcorrelation, respectively. Missing values are handled using the pairwise.complete.obs option.
字符串指定要使用的相关性。允许的值是（唯一的缩写）"pearson"和"bicor"，对应的Pearson和bidweight midcorrelation的，分别。处理缺失值pairwise.complete.obs使用选项。
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：power
soft-thresholding power for netwoek construction.
软阈值功率为netwoek建设。
参数：TOMType
one of "none", "unsigned", "signed". If "none", adjacency will be used for clustering. 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 correlations between neighbors.
"none"，"unsigned"，"signed"之一。如果"none"，邻接将用于聚类。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将跟踪邻居之间的相关性的符号。
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：maxPOutliers
only used for corType=="bicor". Specifies the maximum percentile of data that can be considered outliers on either side of the median separately. For each side of the median, if higher percentile than maxPOutliers is considered an outlier by the weight function based on 9*mad(x), the width of the weight function is increased such that the percentile of outliers on that side of the median equals maxPOutliers. Using maxPOutliers=1 will effectively disable all weight function broadening; using maxPOutliers=0 will give results that are quite similar (but not equal to) Pearson correlation.
仅用于corType=="bicor"。指定的最大百分位数的数据是可以考虑的离群值中位数的任一侧上分开。如果在中位数的每一侧，如果更高的百分比maxPOutliers被认为是一个异常值的权重函数基于9*mad(x)，权重函数的宽度的增加，离群值的那侧上的百分中位数等于maxPOutliers。使用maxPOutliers=1将有效地禁用所有的权重函数扩大; maxPOutliers=0给出的结果是相当类似（但不等于）Pearson相关。
参数：quickCor
real number between 0 and 1 that controls the handling of missing data in the calculation of correlations. See details.
0和1之间，控制处理中丢失的数据的相关性的计算的实数。查看详细信息。
参数：pearsonFallback
Specifies whether the bicor calculation, if used, should revert to Pearson when median absolute deviation (mad) is zero. Recongnized values are (abbreviations of) "none", "individual", "all". If set to "none", zero mad will result in NA for the corresponding correlation. If set to "individual", Pearson calculation will be used only for columns that have zero mad. If set to "all", the presence of a single zero mad will cause the whole variable to be treated in Pearson correlation manner (as if the corresponding robust option was set to FALSE). Has no effect for Pearson correlation. See bicor.
指定是否BICOR计算，如果使用的话，应恢复时，Pearson的平均绝对偏差（MAD）是零。株型识别的值是（的缩写）"none", "individual", "all"。如果设置为"none"，零狂会导致NA相应的相关。如果设置为"individual"，皮尔森计算将仅用于列具有零狂。如果设置为"all"，一个单独的零狂的存在，将导致在Pearson相关性的方式来对待整个变量（如果相应的robust选项被设置为FALSE）。有没有影响Pearson相关。见bicor。
参数：cosineCorrelation
logical: should the cosine version of the correlation calculation be used? The cosine calculation differs from the standard one in that it does not subtract the mean.
余弦版本的相关计算逻辑：应使用？的余弦计算不同于标准的一个，它并没有减去均值。
参数：nThreads
non-negative integer specifying the number of parallel threads to be used by certain parts of correlation calculations. This option only has an effect on systems on which a POSIX thread library is available (which currently includes Linux and Mac OSX, but excludes Windows). If zero, the number of online processors will be used if it can be determined dynamically, otherwise correlation calculations will use 2 threads.
非负的整数，用于指定要使用的某些部分的相关性计算的并行线程的数目。此选项仅影响的系统上POSIX线程库（目前包括Linux和Mac OSX，但不包括视窗）。如果为零，则在线的处理器的数目将被使用，如果是可以动态地确定，否则将使用相关计算2个线程。
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。
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----------
Analysis", Statistical Applications in Genetics and Molecular Biology: Vol. 4: No. 1, Article 17
参见----------See Also----------
TOMsimilarity
TOMsimilarity
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。
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发表于 2012-10-1 22:24:59
