extract_gene_categories: extract_gene_categories

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

Description

This function extracts sets of

1. highly essential genes (essentiality level II, the posterior distribution of the essentiality is shifted less than 1/3 compared to a typical core-essential gene with with FDR of 0.05, unless a different FDR is specified

2. genes confidently not nonessential with FDR of 0.01, unless a different FDR is specified (essentiality level I)

Usage

extract_gene_categories(
  extracted_output,
  FDR_II = 0.05,
  FDR_I = 0.05,
  figures = T
)

Arguments

extracted_output	output of the function extract_from_output
FDR_II	set to 0.05 by default; false positive rate for essentiality of type II
FDR_I	false positive rate for essentiality of type I; set to 0.05 by default

Value

essential_genes_II genes of essentiality level II (see above) essential_genes_I genes of essentiality level I (see above). proportion_core_essential_in_essential_II which proportion of core essential genes is in the essential genes II group (as core essential genes we use the intersection of core essential genes from Hart and Moffat (2016) and Behan et al. (2019)) proportion_core_essential_in_essential_I proportion of core essential genes in essential I group proportion_non_essential_genes_in_essential_II proportion of nonessential genes in essential II group (nonessential as in Hart and Moffat (2016)); this number should be zero or very close to 0 proportion_non_essential_genes_in_essential_I proportion of nonessential genes in essential I group score A summary score for the ability of a screen to separate core essential and nonessential genes.

References

Hart T, Moffat J. BAGEL: a computational framework for identifying essential genesfrom pooled library screens. BMC Bioinformatics. 2016;17(1):164. doi:10.1186/s12859-016-1015-8 Behan FM et al. Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens. Nature. 2019;568(7753):511–516

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