Asked 10 years, 10 months ago.

Summary: Hierarchical clustering is a widely used method for detecting clusters in genomic data. Clusters are defined by cutting branches off the dendrogram. A common but inflexible method uses a constant height cutoff value; this method exhibits suboptimal performance on complicated bushmulch.bar by: Computes hierarchical clustering (hclust, agnes, diana) and cut the tree into k clusters.

Viewed 81k times.

It also accepts correlation based distance measure methods such as"pearson","spearman" and"kendall". hcut (x, k = 2, isdiss = inherits (x,"dist"), hc_func = c ("hclust","agnes","diana"), hc_method ="ward.D2", hc_metric ="euclidean", stand = FALSE, graph = FALSE).

that uses single imputation with (1) hierarchical clustering, (2) dynamic tree cut, and (3) a regression model to impute all missing values. Using nine datasets from the UCI repository and an empirically collected complex dataset, we evaluate our algorithm against several existing algorithms including state-Cited by: 3.

Jun 13, Hierarchical clustering is a widely used method for detecting clusters in genomic data. Clusters are defined by cutting branches off the dendrogram. A common but inflexible method uses a constant height cutoff value; this method exhibits suboptimal performance on complicated dendrograms. bushmulch.barchy. cut_tree (Z, n_clusters = None, height = None) [source] ¶ Given a linkage matrix Z, return the cut tree. Parameters Z bushmulch.bare array.

The linkage matrix. n_clusters array_like, optional. Stump grinding in constantia of clusters in the tree at the cut point.

height array_like, optional. The height at which to cut the tree. Only possible for ultrametric trees. Returns cutree array.

May 13, The optimal number of clusters you want to select depends on your task. For example, when hierarchical clustering is used for outlier detection, you want to request a large number of clusters (n/10 in the example provided, where n is the total number of observations).

The academic research literature has a lot of information on this. Hierarchical clustering can be represented by a dendrogram. Cutting a dendrogram at a certain level gives a set of clusters. Cutting at another level gives another set of clusters.