select_cell_lines: Select mutant groups based on input gene of interest

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

Select mutant groups based on input gene of interest

Description

select_cell_lines() assigns cancer cell lines to either Control groups or one of the following mutant groups: HomDel, T-HetDel, HetDel, Amplified, or Others (see details).

Usage

select_cell_lines(
  input_gene = NULL,
  input_aa_change = NULL,
  input_disease = NULL,
  input_disease_subtype = NULL,
  data_dir = NULL
)

Arguments

input_gene	string as Hugo Symbol
input_aa_change	string Amino acid change (eg. "A387A"). input_gene must be specified
input_disease	string Cancer type listed in list_available_cancer_types()
input_disease_subtype	string Cancer subtype listed in list_available_cancer_subtypes()
data_dir	string Path to GINIR_data

Details

Mutant groups in more detail when only input_gene is defined:

• Control cell lines do not harbor any single nucleotide variations (SNVs) or insertions and deletions (InDels) with a neutral copy number (CN).

• HomDel cell lines harbor one or more homozygous deleterious SNVs or have deep CN loss.

• T-HetDel cell lines harbor two or more heterozygous deleterious SNVs/InDels with neutral or CN loss.

• HetDel cell lines harbor one heterozygous deleterious SNV/InDel with neutral CN, or no SNV/InDel with CN loss.

• Amplified cell lines harbor no SNVs/InDels with increased CN.

• Others cell lines harbor deleterious SNVs with increased CN.

If input_aa_change' is also defined:

• Control cell lines do not harbor any single nucleotide variations (SNVs) or insertions and deletions (InDels) with a neutral copy number (CN).

• HomAlt cell lines harbor a homozygous alteration for the specified mutation.

• HetAlt cell lines harbor a heterozygous alteration for the specified mutation.

• ⁠_CNneutral⁠, ⁠_CNamplified⁠, and ⁠_CNloss⁠ define copy number (CN) status of the above mutation states.

• Others cell lines that do not meet above criteria.

Value

Data frame containing a summary of mutations found in cell lines and their control and mutant group assignments.

Examples

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

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

select_cell_lines(input_gene = "ARID1A", 
input_disease = "Lung Cancer", 
data_dir = gretta_data_dir)

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