get_depmap_plot_data: Create DepMap dataframe for plotting

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

Create DepMap dataframe for plotting

Description

Based on the requested data type, this function will create a dataframe from the DepMap database that can be used for plotting.

Usage

get_depmap_plot_data(gene, data.type, depmap.meta, depmap.pool)

Arguments

gene	Character scalar of gene name.
data.type	Character scalar of data type to retrieve. One of "dependency", "crispr", "rnai", "cn", or "ccle_tpm".
depmap.meta	data.frame of DepMap cell line metadata, as stored in the 'meta' table of the SQLite database built by build_depmap_db.
depmap.pool	pool connection to DepMap SQLite database built with build_depmap_db.

Value

data.frame containing appropriate DepMap data for plotting.

Author(s)

Jared Andrews

See Also

plot_depmap_lineages

Examples

## Not run: 
library(CRISPRball)
build_depmap_db(retrieve = c("meta", "crispr"))
pool <- pool::dbPool(RSQLite::SQLite(), dbname = "depmap_db.sqlite")
depmap.meta <- pool::dbGetQuery(pool, "SELECT * FROM 'meta'")

df <- get_depmap_plot_data(
    gene = "CDK2", data.type = "crispr",
    depmap.meta = depmap.meta, depmap.pool = pool
)

## End(Not run)

j-andrews7/CRISPRball documentation built on Nov. 30, 2023, 7:34 p.m.