print() prints information about the dataset and the status of the analysis to the console. The output contains several fields: Attributes of the data (summarizing key features of the data), Analysis status (indicating the analysis functions that have been called), Analysis parameters (summarizing the analysis parameters set in set_analysis_parameters()), gRNA-to-cell assignment information (summarizing the outcome of the gRNA-to-cell assignment step), and Summary of results (summarizing the key analysis results). A subset of these fields may be printed, depending on the status of the analysis.
Usage
# S4 method for sceptre_object
print(x)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
)
print(sceptre_object)
#> An object of class sceptre_object.
#>
#> Attributes of the data:
#> • 45919 cells
#> • 526 responses
#> • High multiplicity-of-infection
#> • 70 targeting gRNAs (distributed across 35 targets)
#> • 25 non-targeting gRNAs
#> • 6 covariates (batch, grna_n_nonzero, grna_n_umis, response_n_nonzero, response_n_umis, response_p_mito)
#>
#> Analysis status:
#> ✓ import_data()
#> ✗ set_analysis_parameters()
#> ✗ assign_grnas()
#> ✗ run_qc()
#> ✗ run_calibration_check()
#> ✗ run_power_check()
#> ✗ run_discovery_analysis()
#>
#> Analysis parameters:
#> • Discovery pairs: not specified
#> • Positive control pairs: not specified
#> • Sidedness of test: not specified
#> • Resampling mechanism: not specified
#> • gRNA integration strategy: not specified
#> • Resampling approximation: not specified
#> • Multiple testing adjustment: none
#> • N nonzero treatment cells threshold: not specified
#> • N nonzero control cells threshold: not specified
#> • Formula object: not specified