build_depmap_db: Build SQLite database of DepMap data

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

Build SQLite database of DepMap data

Description

Build SQLite database of DepMap data

Usage

build_depmap_db(
  retrieve = c("rnai", "crispr", "dependency", "cn", "ccle_tpm", "meta", "drug",
    "gene.summary", "release"),
  file = "depmap_db.sqlite"
)

Arguments

retrieve

Character vector of data to retrieve from DepMap. Options include: rnai: RNAi screen data from depmap_rnai. crispr: CRISPR screen data from depmap_crispr. cn: Copy number data from depmap_copyNumber. ccle_tpm: TPM data from depmap_TPM. meta: Cell line metadata from depmap_metadata. drug: Drug sensitivity data from depmap_drug_sensitivity. gene.summary: Gene summary data from depmap_gene_summary. release: DepMap release information from from depmap_release.

file

Name of SQLite database file to create.

Value

Name of SQLite database containing DepMap data.

Author(s)

Jared Andrews

See Also

depmap_rnai, depmap_crispr, depmap_copyNumber, depmap_TPM, depmap_metadata, depmap_gene_summary, depmap_drug_sensitivity, depmap_release dbPool, dbWriteTable

Examples

library(CRISPRball)
build_depmap_db(retrieve = "release")

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