Covariate matrix

A matrix of cell-specific technical factors:

lg_gRNA_lib_size

(numeric) log-transformed gRNA library size

lg_gene_lib_size

(numeric) log-transformed gene library size

p_mito

(numeric) fraction of sequenced gene transcripts that map to mitochondrial genes

batch

(factor) sequencing batch (batch_1, batch_2)

data(covariate_matrix)

Format

An object of class data.frame with 40000 rows and 4 columns.

Overview

This object is part of the example data. The data are taken from the paper "A genome-wide framework for mapping gene regulation via cellular genetic screens" by Gasperini et al., 2019. The authors used a CRISPRi-based assay to target 5,000+ putative enhancers in a population of K562 cells. The authors additionally targeted 200+ gene transcription start sites (TSSs) and designed a library of 50 non-targeting gRNAs to serve as negative controls. Genes, gRNAs, and cells are all down-sampled to reduce the size of the data.