get_depmap_essentiality: Get essential/selective gene information from DepMap summary...

In j-andrews7/CRISPRball: Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

Get essential/selective gene information from DepMap summary table.

Description

Get essential/selective gene information from DepMap summary table.

Usage

get_depmap_essentiality(gene, depmap.summary)

Arguments

gene	Character scalar for gene symbol.
depmap.summary	data.frame containing DepMap gene summary information.

Value

Named list containing RNAi and CRISPR named lists containing dataset information for the provided gene, if available. If the gene is not found in the summary data.frame, the avail element for the RNAi and CRISPR lists will be set to FALSE.

Author(s)

Jared Andrews

Examples

library(CRISPRball)
build_depmap_db(retrieve = "gene.summary")
pool <- pool::dbPool(RSQLite::SQLite(), dbname = "depmap_db.sqlite")
depmap.gene <- pool::dbGetQuery(pool, "SELECT * FROM 'gene.summary'")

essentials <- get_depmap_essentiality(gene = "CDK2", depmap.summary = depmap.gene)

j-andrews7/CRISPRball documentation built on Nov. 8, 2024, 2:43 a.m.