extract_prot: Extract protein expression data for given cell lines

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

Extract protein expression data for given cell lines

Description

FUNCTION_DESCRIPTION

Usage

extract_prot(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) encoding proteins of interest, Default: NULL
data_dir	string Path to GINIR_data

Details

See also extract_protein_rna to extract proteomics profile data

Value

Data frame containing protein expression for samples provided in the input. If no genes were specified, the function will return a data frame of proteins 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_prot(
input_samples = c('ACH-000004', 'ACH-000146'), 
input_genes = c('CIC'),
data_dir = gretta_data_dir)

ytakemon/GINIR documentation built on Oct. 11, 2024, 6:06 a.m.