bin: Subfunction of bin_metadata() for expression/positional...

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

Subfunction of bin_metadata() for expression/positional binning

Description

This function computes a pseudospatial distance between beads that combines spatial distance and distance from the expression space, then using the silhouette score and hierarchical clustering, segregates beads into bins

Usage

bin(
  dat,
  md,
  k,
  pos = TRUE,
  pos_k = 55,
  ex_k = 1,
  hc_function = "ward.D2",
  plot_directory
)

Arguments

dat	data.table of smoothed relative expression intensities
md	data.table of metadata of each bead
k	number of malignant bins to set
pos	TRUE if doing spatial and expressional binning, FALSE if just expressional binning
pos_k	positional weight
ex_k	expressional weight
hc_function	hierarchical clustering function
plot_directory	output plot directory path

Value

A data.table of bead metadata combined with bin designations

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