construct_positive_control_pairs: Construct positive control pairs

In Katsevich-Lab/sceptre: Analysis of Single-Cell CRISPR Screen Data

Construct positive control pairs

Description

construct_positive_control_pairs() is a helper function to facilitate construction of the positive control pairs. Positive control pairs are target-response pairs for which we know (or have strong reason to believe) that there is a regulatory relationship between the target and the response. We can use positive control pairs to verify that sceptre is sensitive (i.e., capable of detecting true associations) on the dataset under analysis. construct_positive_control_pairs() takes as an argument a sceptre_object and returns a data frame with columns grna_target and response_id, where gRNA targets and response IDs with matching names are paired. Typically, the positive control set consists of transcription start sites paired to the gene regulated by those transcription start sites. See Section 2.2 in the manual for more detailed information about this function.

Usage

construct_positive_control_pairs(sceptre_object)

Arguments

sceptre_object

a sceptre_object

Value

a data frame with columns grna_target and response_id containing the positive control pairs

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)

Katsevich-Lab/sceptre documentation built on Nov. 19, 2024, 5:16 p.m.