reconstruct: Apply a clustering algorithm to a given time course.

In MultIS: Reconstruction of Clones from Integration Site Readouts and Visualization

Description

Apply a clustering algorithm to a given time course.

Usage

reconstruct(
  readouts,
  target_communities,
  method = "kmedoids",
  sim = MultIS::get_similarity_matrix(readouts = readouts, upper = TRUE),
  cluster_obj = FALSE
)

Arguments

readouts	The time course for which to find clusters.
target_communities	The number of clusters to cluster for.
method	Either "kmedoids", "kmeans" or any string permitted as a method for stats::hclust.
sim	A similarity matrix used with all methods except "kmeans".
cluster_obj	If TRUE, a clusterObject with the readouts, similarity and clustering is returned.

Value

A matrix with two columns: "Clone" and "IS" or if cluster_obj = TRUE a cluster object, which can be used to plot the clustering.

MultIS documentation built on Aug. 6, 2021, 5:07 p.m.