Run ShallowHRD on a QDNAseq object. — RunShallowHRDFromQDNA • utanos

This function takes a QDNAseqCopyNumbers object, extracts the binned and segmented copy-number data, and runs ShallowHRD on each sample.

Usage

RunShallowHRDFromQDNA(
  qdna_obj,
  include_chr_X = FALSE,
  num_simulations = 1e+05,
  shrd_save_path = FALSE,
  plot = FALSE,
  seed = 1337,
  cores = 1,
  log_transform = TRUE
)

Arguments

qdna_obj: An S4 object of type QDNAseqCopyNumbers. This object must contain a copynumber slot and a segmented slot.
include_chr_X: Whether or not to include the X-chromosome when running ShallowHRD.
num_simulations: The number of simulations to use during the FindThreshold() step.
shrd_save_path: An optional path to save the ShallowHRD results to.
plot: Whether or not to return a plot showing how segments are merged as the algorithm runs.
seed: A seed to use for PRNG-dependent functions. Ensures reproduciblity between runs.
cores: The number of cores to use for running samples in parallel. If set to 1, no parallel processing will be used.

Value

A list of ShallowHRD results, with one entry per sample.