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Run discovery analysis

Source: R/s4_analysis_functs_2.R
run_discovery_analysis.Rd

run_discovery_analysis() runs the discovery analysis. The discovery analysis involves applying sceptre to analyze discovery pairs, or target-response pairs whose association status we do not know but seek to learn. Identifying associations among the discovery pairs is the primary objective of the single-cell CRISPR screen analysis. See Chapter 6 of the manual for more detailed information about this function.

Usage

run_discovery_analysis(
  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 discovery analysis 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
discovery_pairs <- construct_cis_pairs(sceptre_object)
sceptre_object <- sceptre_object |>
  set_analysis_parameters(
    side = "left",
    resampling_mechanism = "permutations",
    discovery_pairs = discovery_pairs
  ) |>
  assign_grnas(method = "thresholding") |>
  run_qc() |>
  run_discovery_analysis(
    parallel = TRUE,
    n_processors = 2
  )
#> Warning: The calibration check (`run_calibration_check()`) should be run before the discovery analysis.
#> 
#> Generating permutation resamples. ✓
#> Running discovery_analysis in parallel. Change directories to /var/folders/7v/5sqjgh8j28lgf8qx3gbtq1h00000gp/T//RtmpHhxNRw/sceptre_logs/ and view the files discovery_analysis_*.out for progress updates.
#>  ✓
#>