get_GeneNameID: Get unique DepMap-compatible gene IDs

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

Get unique DepMap-compatible gene IDs

Description

get_GeneNameID() and get_DepMapID() provide tools for converting gene symbols/ids and common cell line aliases to DepMap's unique gene name and cell line identifiers, respectively.

Usage

get_GeneNameID(gene_name, data_dir)

get_DepMapID(sample_name, data_dir)

Arguments

gene_name	string containing a vector of either Hugo gene symbol or numeric NCBI ID
data_dir	string Path to GINIR_data
sample_name	string containing a vector of unique sample_id used in proteomics data or common cell line names

Value

string

string

Functions

• get_DepMapID(): Get unique DepMap-compatible sample IDs

Examples

gretta_data_dir <- './GRETTA_example/'
gretta_output_dir <- './GRETTA_example_output/'

if(!dir.exists(gretta_data_dir)){
  download_example_data(".")
}

get_GeneNameID('A1CF', data_dir = gretta_data_dir)

gretta_data_dir <- './GRETTA_example/'
gretta_output_dir <- './GRETTA_example_output/'

if(!dir.exists(gretta_data_dir)){
  download_example_data(".")
}

get_DepMapID('JURKAT', data_dir = gretta_data_dir)

ytakemon/GINIR documentation built on Feb. 27, 2024, 1:33 p.m.