Package 'WGCNA' - Laboratory Web Sites - UCLA
Package 'WGCNA' - Laboratory Web Sites - UCLA
Package 'WGCNA' - Laboratory Web Sites - UCLA
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20 blockwiseModules<br />
randomSeed<br />
corType<br />
power<br />
integer to be used as seed for the random number generator before the function<br />
starts. If a current seed exists, it is saved and restored upon exit. If NULL is<br />
given, the function will not save and restore the seed.<br />
character string specifying the correlation to be used. Allowed values are (unique<br />
abbreviations of) "pearson" and "bicor", corresponding to Pearson and<br />
bidweight midcorrelation, respectively. Missing values are handled using the<br />
pairwise.complete.obs option.<br />
soft-thresholding power for network construction.<br />
networkType network type. Allowed values are (unique abbreviations of) "unsigned",<br />
"signed", "signed hybrid". See adjacency.<br />
TOMType<br />
one of "none", "unsigned", "signed". If "none", adjacency will be<br />
used for clustering. If "unsigned", the standard TOM will be used (more<br />
generally, TOM function will receive the adjacency as input). If "signed",<br />
TOM will keep track of the sign of correlations between neighbors.<br />
deepSplit integer value between 0 and 4. Provides a simplified control over how sensitive<br />
module detection should be to module splitting, with 0 least and 4 most sensitive.<br />
See cutreeDynamic for more details.<br />
detectCutHeight<br />
dendrogram cut height for module detection. See cutreeDynamic for more<br />
details.<br />
minModuleSize<br />
minimum module size for module detection. See cutreeDynamic for more<br />
details.<br />
maxCoreScatter<br />
maximum scatter of the core for a branch to be a cluster, given as the fraction of<br />
cutHeight relative to the 5th percentile of joining heights. See cutreeDynamic<br />
for more details.<br />
minGap minimum cluster gap given as the fraction of the difference between cutHeight<br />
and the 5th percentile of joining heights. See cutreeDynamic for more details.<br />
maxAbsCoreScatter<br />
maximum scatter of the core for a branch to be a cluster given as absolute<br />
heights. If given, overrides maxCoreScatter. See cutreeDynamic for<br />
more details.<br />
minAbsGap<br />
minimum cluster gap given as absolute height difference. If given, overrides<br />
minGap. See cutreeDynamic for more details.<br />
pamStage logical. If TRUE, the second (PAM-like) stage of module detection will be<br />
performed. See cutreeDynamic for more details.<br />
pamRespectsDendro<br />
Logical, only used when pamStage is TRUE. If TRUE, the PAM stage will<br />
respect the dendrogram in the sense an object can be PAM-assigned only to<br />
clusters that lie below it on the branch that the object is merged into. See<br />
cutreeDynamic for more details.<br />
minKMEtoJoin a number between 0 and 1. Genes with eigengene connectivity higher than<br />
minKMEtoJoin are automatically assigned to their closest module.<br />
minCoreKME<br />
a number between 0 and 1. If a detected module does not have at least minModuleKMESize<br />
genes with eigengene connectivity at least minCoreKME, the module is disbanded<br />
(its genes are unlabeled and returned to the pool of genes waiting for<br />
mofule detection).
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