reconstruct {MultIS}

Apply a clustering algorithm to a given time course.

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.