Description Usage Arguments Value
Module detection for an individual tree
1 2 3 | cut_dendro(tree_dendro, min_cluster_size = 2L, datan, ME_diss_thres,
name_of_tree = "", qc_plot = TRUE, n_pc = 1, robust_PCs = FALSE,
nb_min_varExpl = 0.5, method = c("pearson", "kendall", "spearman"))
|
tree_dendro |
List of tree specific objects including dendrogram, tree data and features originating from the tree_dendro function. |
min_cluster_size |
Integer. The minimum number of features in one module. |
datan |
Data frame were rows correspond to samples and columns to features. |
ME_diss_thres |
Numeric. Module Eigengene Dissimilarity Threshold for merging close modules. |
name_of_tree |
String. Annotating plots and messages. |
qc_plot |
Logical. Should plots be created? |
n_pc |
Number of principal components and variance explained entries to be calculated. The number of returned variance explained entries is currently ‘min(n_pc,10)’. If given ‘n_pc’ is greater than 10, a warning is issued. |
robust_PCs |
Should PCA be calculated on ranked data (Spearman PCA)? Rotations will not correspond to original data if this is applied. |
nb_min_varExpl |
Minimum proportion of variance explained for returned module eigengenes. The number of PCs is capped at n_pc. |
method |
A character string specifying the method to be used for correlation coefficients. |
List
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