create_small_subset: create_small_subset This function takes as input a matrix of...

In magStra/BSure: What the Package Does (One Line, Title Case)

Description

create_small_subset This function takes as input a matrix of count data from a CRISPR screen and returns a smaller subset containing 20 core essential and 20 nonessential genes, as well as 20 genes known to be differentially essential across different (cancer) cell lines (Behan et al., 2019). The purpose of this function is to create a small sample dataset to illustrate the method.

Usage

create_small_subset(counts)

Arguments

counts

Mx(R+2) matrix or data frame of gRNA counts, where M is the number of gRNAs and R the number of replicates, the first column of the matrix contains the names of the gRNAs, the second gene names or identifiers corresponding to the gRNAs in the first column

Value

reduced matrix of gRNA counts, containing 20 core-essential genes, 20 nonessential genes, and 20 genes know to be differentially essential across different (cancer) cell lines

References

Behan FM et al. Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens. Nature. 2019;568(7753):511–516.

Examples

data("counts_HT29")
counts_HT29_small_subset <- create_small_subset(counts_HT29)

magStra/BSure documentation built on April 27, 2021, 3:30 a.m.