write_outputs_to_directory() writes the outputs of a sceptre analysis to a directory on disk. write_outputs_to_directory() writes several files to the specified directory: a text-based summary of the analysis (analysis_summary.txt), the various plots (*.png), the calibration check, power check, discovery analysis results (results_run_calibration_check.rds, results_run_power_check.rds, and results_run_discovery_analysis.rds, respectively), and the binary gRNA-to-cell assignment matrix (grna_assignment_matrix.rds). See Section 8 of the introductory chapter in the manual for more information about this function.
Arguments
- sceptre_object
a
sceptre_object- directory
a string giving the file path to a directory on disk in which to write the results
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
)
positive_control_pairs <- construct_positive_control_pairs(sceptre_object)
discovery_pairs <- construct_cis_pairs(sceptre_object,
positive_control_pairs = positive_control_pairs,
distance_threshold = 5e6
)
sceptre_object |>
set_analysis_parameters(
side = "left",
resampling_mechanism = "permutations",
discovery_pairs = discovery_pairs,
positive_control_pairs = positive_control_pairs
) |>
assign_grnas(method = "thresholding") |>
run_qc() |>
run_calibration_check(
parallel = TRUE,
n_processors = 2
) |>
run_power_check() |>
run_discovery_analysis(
parallel = TRUE,
n_processors = 2
) |>
write_outputs_to_directory(paste0(tempdir(), "/sceptre_outputs"))
#> NULL
# files written to "sceptre_outputs" in tempdir()