get_num_clust: Find optimal number of clusters

In dkzhang777/SlideCNA: Calls Copy Number Alterations from Slide-Seq Data

Find optimal number of clusters

Description

This function uses the Silhouette Method applied to CNV scores to determine the best number of clusters to divide the binned beads into

Usage

get_num_clust(
  data,
  hc_func = "ward.D2",
  max_k = 10,
  plot = TRUE,
  malig = FALSE,
  k = NA,
  plot_directory
)

Arguments

data	cnv_data list object of cnv data from SlideCNA::prep_cnv_dat()
hc_func	character string for which hierarchical clustering function to use
max_k	integer of number max number of clusters to evaluate (2:max_k)
plot	TRUE if plotting silhoutte scores per cluster
malig	TRUE if only using malignant bins and FALSE if using all bins
k	integer of optimal number of clusters, if known, and NA if not known
plot_directory	output plot directory path

Value

An integer representing the number of clusters that optimizes the silhouette score

dkzhang777/SlideCNA documentation built on Jan. 25, 2025, 5:53 p.m.