extract_rna: Extract RNA expression data for given cell lines

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

Extract RNA expression data for given cell lines

Description

FUNCTION_DESCRIPTION

Usage

extract_rna(input_samples = NULL, input_genes = NULL, data_dir = NULL)

Arguments

input_samples	string A vector of DepMap_ID(s) must be provided, Default: NULL
input_genes	string Optional Hugo Symbol(s), Default: NULL
data_dir	string Path to GINIR_data

Details

See also extract_prot to extract proteomics profile data

Value

Data frame containing RNA expression (TPM) for sample provided in the input. If no genes were specified, the function will return a data frame of all genes profiled in DepMap

Examples

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

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

extract_rna(
input_samples = c('ACH-001642','ACH-000688'), 
input_genes = c('ARID1A'),
data_dir = gretta_data_dir)

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