recutConsensusTrees(WGCNA)
recutConsensusTrees()所属R语言包：WGCNA
Repeat blockwise consensus module detection from pre-calculated data
从预先计算的数据重复列块的共识模块检测
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Given consensus networks constructed for example using blockwiseConsensusModules, this function (re-)detects modules in them by branch cutting of the corresponding dendrograms. If repeated branch cuts of the same gene network dendrograms are desired, this function can save substantial time by re-using already calculated networks and dendrograms.
鉴于共识网络构造例如使用blockwiseConsensusModules，这个函数（重新）检测在他们的模块，由分支切割相应的聚类。如果需要重复相同的基因网络系统树的分支切割，此功能可以节省大量的时间，通过重新使用已计算的网络和系统树。
用法----------Usage----------
recutConsensusTrees(
multiExpr,
goodSamples, goodGenes,
blocks,
TOMFiles,
dendrograms,
corType = "pearson",
networkType = "unsigned",
deepSplit = 2,
detectCutHeight = 0.995, minModuleSize = 20,
checkMinModuleSize = TRUE,
maxCoreScatter = NULL, minGap = NULL,
maxAbsCoreScatter = NULL, minAbsGap = NULL,
pamStage = TRUE, pamRespectsDendro = TRUE,
trimmingConsensusQuantile = 0,
minCoreKME = 0.5, minCoreKMESize = minModuleSize/3,
minKMEtoStay = 0.2,
reassignThresholdPS = 1e-4,
mergeCutHeight = 0.15,
mergeConsensusQuantile = trimmingConsensusQuantile,
impute = TRUE,
trapErrors = FALSE,
numericLabels = FALSE,
verbose = 2, indent = 0)
参数----------Arguments----------
参数：multiExpr
expression data in the multi-set format (see checkSets). A vector of lists, one per set. Each set must contain a component data that contains the expression data, with rows corresponding to samples and columns to genes or probes.
表达在多集的格式的数据（见checkSets）。一个向量的列表，每一个组。每个集必须包含一个组件data包含的表达数据，与对应的基因或探针的样品和列的行。
参数：goodSamples
a list with one component per set. Each component is a logical vector specifying which samples are considered "good" for the analysis. See goodSamplesGenesMS.
用的一个组成部分，每一套的列表。每个组件是一个逻辑向量指定的样品被认为是“好”的分析。见goodSamplesGenesMS。
参数：goodGenes
a logical vector with length equal number of genes in multiExpr that specifies which genes are considered "good" for the analysis. See goodSamplesGenesMS.
逻辑向量长度相等数目的基因在multiExpr指定哪些基因被认为是“好”的分析。见goodSamplesGenesMS。
参数：blocks
specification of blocks in which hierarchical clustering and module detection should be performed. A numeric vector with one entry per gene of multiExpr giving the number of the block to which the corresponding gene belongs.
规格层次聚类和模块检测应执行块。甲数值向量multiExpr给出的块的数目，相应的基因属于每个基因的一个条目。
参数：TOMFiles
a vector of character strings specifying file names in which the block-wise topological overlaps are saved.
一个向量的字符串指定的文件名保存在其中的块单位的拓扑重叠。
参数：dendrograms
a list of length equal the number of blocks, in which each component is a hierarchical clustering dendrograms of the genes that belong to the block.
的列表的长度等于块组成，其中每个组件是一个层次聚类的聚类的基因，属于该块的数目。
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 pariwise.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pariwise.complete.obs使用选项。
参数：networkType
network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid". See adjacency. Note that while no new networks are computed in this function, this parameter affects the interpretation of correlations in this function.
网络类型。允许的值是（）"unsigned"，"signed"，"signed hybrid"唯一的缩写。见adjacency。需要注意的是，在这个函数中，而没有新的网络计算，此参数会影响此功能的相关性的解释。
参数：deepSplit
integer value between 0 and 4. Provides a simplified control over how sensitive module detection should be to module splitting, with 0 least and 4 most sensitive. See cutreeDynamic for more details.
在0和4之间的整数值。应该是敏感的模块检测到模块的分裂提供了一个简化的控制，与0至少4个最敏感的。见cutreeDynamic更多详情。
参数：detectCutHeight
dendrogram cut height for module detection. See cutreeDynamic for more details.
模块检测系统树砍高度。见cutreeDynamic更多详情。
参数：minModuleSize
minimum module size for module detection. See cutreeDynamic for more details.
模块检测最小的模块尺寸。见cutreeDynamic更多详情。
参数：checkMinModuleSize
logical: should sanity checks be performed on minModuleSize?
逻辑上进行完整性检查minModuleSize？
参数：maxCoreScatter
maximum scatter of the core for a branch to be a cluster, given as the fraction of cutHeight relative to the 5th percentile of joining heights. See cutreeDynamic for more details.
最大散度为核心的一个分支，是一个聚类，cutHeight相对于第5百分位加盟高度的比例。见cutreeDynamic更多详情。
参数：minGap
minimum cluster gap given as the fraction of the difference between cutHeight and the 5th percentile of joining heights. See cutreeDynamic for more details.
给出最小聚类隙作为cutHeight和高度的接合的第5百分位之间的差异的馏分。见cutreeDynamic更多详情。
参数：maxAbsCoreScatter
maximum scatter of the core for a branch to be a cluster given as absolute heights. If given, overrides maxCoreScatter. See cutreeDynamic for more details.
最大散度为核心的一个分支，是一个绝对高度聚类。如果给定的，覆盖maxCoreScatter。见cutreeDynamic更多详情。
参数：minAbsGap
minimum cluster gap given as absolute height difference. If given, overrides minGap. See cutreeDynamic for more details.
最小群的差距给予作为绝对高度差。如果给定的，覆盖minGap。见cutreeDynamic更多详情。
参数：pamStage
logical. If TRUE, the second (PAM-like) stage of module detection will be performed. See cutreeDynamic for more details.
逻辑。如果是TRUE，第二阶段（PAM等）的模块检测将被执行。见cutreeDynamic更多详情。
参数：pamRespectsDendro
Logical, only used when pamStage is TRUE. If TRUE, the PAM stage will respect the dendrogram in the sense an object can be PAM-assigned only to clusters that lie below it on the branch that the object is merged into. See cutreeDynamic for more details.
逻辑，只用时pamStage是TRUE。如果TRUE，PAM阶段会尊重树状图在这个意义上，一个对象可以是PAM-分配到聚类位于它下面的对象被合并到分支。见cutreeDynamic更多详情。
参数：trimmingConsensusQuantile
a number between 0 and 1 specifying the consensus quantile used for kME calculation that determines module trimming according to the arguments below.
0和1之间的一个数，指定的共识用于KME计算的位数，确定模块，修整根据下面的论据。
参数：minCoreKME
a number between 0 and 1. If a detected module does not have at least minModuleKMESize genes with eigengene connectivity at least minCoreKME, the module is disbanded (its genes are unlabeled and returned to the pool of genes waiting for mofule detection).
0和1之间的一个数。如果检测到的模块不与eigengene连接至少有minModuleKMESize基因至少minCoreKME，该模块被解散（未标记的基因，并返回到池中等待mofule检测的基因）。
参数：minCoreKMESize
see minCoreKME above.
看到minCoreKME以上。
参数：minKMEtoStay
genes whose eigengene connectivity to their module eigengene is lower than minKMEtoStay are removed from the module.
基因的eigengene连接到模块eigengene的是比minKMEtoStay是从模块中删除。
参数：reassignThresholdPS
per-set p-value ratio threshold for reassigning genes between modules. See Details.
每个组的p值比阈值重新分配模块之间的基因。查看详细信息。
参数：mergeCutHeight
dendrogram cut height for module merging.
树图切模块合并的高度。
参数：mergeConsensusQuantile
consensus quantile for module merging. See mergeCloseModules for details.
模块合并的共识位数。见mergeCloseModules的详细信息。
参数：impute
logical: should imputation be used for module eigengene calculation? See moduleEigengenes for more details.
逻辑：应归集使用计算模块eigengene的？见moduleEigengenes更多详情。
参数：trapErrors
logical: should errors in calculations be trapped?
逻辑：应计算错误而陷入吗？
参数：numericLabels
logical: should the returned modules be labeled by colors (FALSE), or by numbers (TRUE)?
逻辑：应返回的模块进行标记的颜色（FALSE），或由数字（TRUE）的？
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----------
For details on blockwise consensus module detection, see blockwiseConsensusModules. This function implements the module detection subset of the functionality of blockwiseConsensusModules; network construction and clustering must be performed in advance. The primary use of this function is to experiment with module detection settings without having to re-execute long network and clustering calculations whose results are not affected by the cutting parameters.
对于列块的共识模块检测的详细信息，请参阅blockwiseConsensusModules。此功能实现模块检测功能的子集blockwiseConsensusModules网络的建设和聚类必须提前进行。此功能的主要用途是实验模块检测设置，而不必重新执行长的网络和聚类计算的切削参数，其结果不会受到影响。
This function takes as input the networks and dendrograms that are produced by blockwiseConsensusModules. Working block by block, modules are identified in the dendrograms by the Dynamic Hybrid tree cut. Found modules are trimmed of genes whose consensus module membership kME (that is, correlation with module eigengene) is less than minKMEtoStay. Modules in which fewer than minCoreKMESize genes have consensus KME higher than minCoreKME are disbanded, i.e., their constituent genes are pronounced unassigned.
此功能需要输入的网络和系统树是由blockwiseConsensusModules。工作一块块模块标识中的树状图的动态混合树切。发现模块被修剪的共识模块成员KME（即，相关模块eigengene）的是小于minKMEtoStay的基因。模块不到minCoreKMESize基因是有共识的KME高于minCoreKME解散，即其组成基因的发音未分配的。
After all blocks have been processed, the function checks whether there are genes whose KME in the module they assigned is lower than KME to another module. If p-values of the higher correlations are smaller than those of the native module by the factor reassignThresholdPS (in every set), the gene is re-assigned to the closer module.
所有块都被处理之后，该函数将检查是否有基因的KME在他们分配模块是低于KME到另一个模块。如果较高的相关性的p-值小于是由因子reassignThresholdPS（在每一个集合），该基因被重新分配到的密切模块的本机模块。
In the last step, modules whose eigengenes are highly correlated are merged. This is achieved by clustering module eigengenes using the dissimilarity given by one minus their correlation, cutting the dendrogram at the height mergeCutHeight and merging all modules on each branch. The process is iterated until no modules are merged. See mergeCloseModules for more details on module merging.
在最后一步中，模块，其特征基因是高度相关的合并。这是通过使用给定的由减去及其相关性之一的相异的聚类模块特征基因，切割mergeCutHeight和合并每个分支上的所有模块的高度在树状图。该过程被重复，直到没有合并模块。见mergeCloseModules模块合并的详细信息。
值----------Value----------
A list with the following components:
以下组件列表：
参数：colors
module assignment of all input genes. A vector containing either character strings with module colors (if input numericLabels was unset) or numeric module labels (if numericLabels was set to TRUE). The color "grey" and the numeric label 0 are reserved for unassigned genes.
所有的输入基因的模块分配。如果输入一个向量，包含模块的颜色是字符的字符串（numericLabels未设置）或数字模块标签（如果numericLabels设置为TRUE的“）。颜色为“灰色”和数字标签0被保留为未分配的基因。
参数：unmergedColors
module colors or numeric labels before the module merging step.
模块的颜色或模块合并步骤之前的数字标签。
参数：multiMEs
module eigengenes corresponding to the modules returned in colors, in multi-set format. A vector of lists, one per set, containing eigengenes, proportion of variance explained and other information. See multiSetMEs for a detailed description.
模块的特征基因对应于返回的模块在colors，在多设置的格式。向量的列表，每一个组，包含特征基因，解释方差比例和其他信息。见multiSetMEs进行了详细的描述。
注意----------Note----------
Basic sanity checks are performed on given arguments, but it is left to the user's responsibility to provide valid input.
在给定的参数进行基本的完整性检查，但它留给用户自己的责任提供有效的输入。
（作者）----------Author(s)----------
Peter Langfelder
参考文献----------References----------
参见----------See Also----------
blockwiseConsensusModules for the full blockwise modules calculation. Parts of its output are natural input for this function.
blockwiseConsensusModules全列块的模块计算。其输出的零件自然输入此功能。
cutreeDynamic for adaptive branch cutting in hierarchical clustering dendrograms;
cutreeDynamic自适应枝扦插层次聚类树状图;
mergeCloseModules for merging of close modules.
mergeCloseModules合并密切模块。
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 22:19:31
