prep_cnv_dat: Prepare data for CNV heat map

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

Prepare data for CNV heat map

Description

This function caps CNV scores, adds annotation columns for plotting, performs hierarchical clustering of bins based on similar CNV score, and plots nUMI per bin

Usage

prep_cnv_dat(
  dat_bin,
  lower = 0.6,
  upper = 1.4,
  hc_function = "ward.D2",
  plot_directory
)

Arguments

dat_bin	data.table of CNV scores per bin
lower	numeric float to represent the lower cap for CNV scores
upper	numeric float to represent the upper cap for CNV scores
hc_function	character for which hierarchical clustering function to use
plot_directory	output plot directory path

Value

A list object for downstream cnv plotting and analysis all = data.table of CNV scores of all bins x (metadata + genes) malig = data.table of CNV scores of just malignant bins x (metadata + genes) all_wide = data.frame in wide format of CNV scores of all bins x (metadata + genes) malig_wide = data.frame in wide format of CNV scores of just malignant bins x (metadata + genes) hcl = hclust object that describes the hierarchical clustering for malignant bins hcl_all = hclust object that describes the hierarchical clustering for all bins

SlideCNA documentation built on April 4, 2025, 1:59 a.m.