run_power_check: Run power check

In timothy-barry/sceptre: Analysis of Single-Cell CRISPR Screen Data

Run power check

Description

run_power_check() runs the power check. The power check entails applying sceptre to analyze positive control pairs — pairs for which we know there is an association between the target and the response — to ensure that sceptre is capable of detecting true associations. See Chapter 6 of the manual for more detailed information about this function.

Usage

run_power_check(
  sceptre_object,
  output_amount = 1,
  print_progress = TRUE,
  parallel = FALSE,
  n_processors = "auto",
  log_dir = tempdir()
)

Arguments

sceptre_object	a sceptre_object
output_amount	(optional; default 1) an integer taking values 1, 2, or 3 specifying the amount of information to return. 1 returns the least amount of information and 3 the most.
print_progress	(optional; default TRUE) a logical indicating whether to print progress updates
parallel	(optional; default FALSE) a logical indicating whether to run the function in parallel
n_processors	(optional; default "auto") an integer specifying the number of processors to use if parallel is set to TRUE. The default, "auto", automatically detects the number of processors available on the machine.
log_dir	(optional; default tempdir()) a string indicating the directory in which to write the log files (ignored if parallel = FALSE)

Value

an updated sceptre_object in which the power check has been carried out

Examples

library(sceptredata)
data(highmoi_example_data)
data(grna_target_data_frame_highmoi)
# import data
sceptre_object <- import_data(
  response_matrix = highmoi_example_data$response_matrix,
  grna_matrix = highmoi_example_data$grna_matrix,
  grna_target_data_frame = grna_target_data_frame_highmoi,
  moi = "high",
  extra_covariates = highmoi_example_data$extra_covariates,
  response_names = highmoi_example_data$gene_names
)

# set analysis parameters, assign grnas, run qc
positive_control_pairs <- construct_positive_control_pairs(sceptre_object)
sceptre_object <- sceptre_object |>
  set_analysis_parameters(
    side = "left",
    resampling_mechanism = "permutations",
    positive_control_pairs = positive_control_pairs
  ) |>
  assign_grnas(method = "thresholding") |>
  run_qc() |>
  run_power_check()

timothy-barry/sceptre documentation built on Sept. 27, 2024, 6:49 a.m.