Function reference • sceptre

Package documentation

sceptre sceptre-package: sceptre

Pipeline functions

The functions that form the basis of the sceptre pipeline

import_data(): Import data

import_data_from_cellranger(): Import data from Cell Ranger

import_data_from_parse(): Import data from Parse (experimental)

set_analysis_parameters(): Set analysis parameters

assign_grnas(): Assign gRNAs to cells

run_qc(): Run QC

run_calibration_check(): Run calibration check

run_power_check(): Run power check

run_discovery_analysis(): Run discovery analysis

Plotting functions

Functions to visualize the analysis

plot(<sceptre_object>): Plot

plot_grna_count_distributions(): Plot gRNA count distributions

plot_assign_grnas(): Plot assign gRNAs

plot_run_qc(): Plot run QC

plot_run_calibration_check(): Plot run calibration check

plot_run_discovery_analysis(): Plot run discovery analysis

plot_run_power_check(): Plot run power check

plot_covariates(): Plot covariates

plot_response_grna_target_pair(): Plot response-gRNA-target pair

Pair constructor functions

Functions to facilitate the construction of discovery pairs and positive control pairs

construct_positive_control_pairs(): Construct positive control pairs

construct_cis_pairs(): Construct cis pairs

construct_trans_pairs(): Construct trans pairs

gene_position_data_frame_grch38 gene_position_data_frame_grch37: Gene position data frames

Information extraction functions

Functions to extract information and results from a sceptre_object

print(<sceptre_object>): Print

write_outputs_to_directory(): Write outputs to directory

get_result(): Get result

get_response_matrix() get_grna_matrix() get_cell_covariates(): Data getter functions

get_grna_assignments(): Get gRNA assignments

`ondisc` intput/output functions

read_ondisc_backed_sceptre_object() write_ondisc_backed_sceptre_object(): Write or read an ondisc-backed sceptre_object

Example data

highmoi_example_data: Example high-MOI data

grna_target_data_frame_highmoi: gRNA target data frame

lowmoi_example_data: Example low-MOI data