list_mutations: Search mutations detected in DepMap cancer cell lines

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

Search mutations detected in DepMap cancer cell lines

Description

Quick method to look up mutations of interest prior to using select_cell_lines()

Usage

list_mutations(
  gene = NULL,
  chr = NULL,
  start_bp = NULL,
  end_bp = NULL,
  is_hotspot = NULL,
  is_damaging = NULL,
  variant_classification = NULL,
  data_dir = NULL
)

Arguments

gene	string, Hugo Symbol, Default: NULL
chr	string, Default: NULL
start_bp	integer, Default: NULL
end_bp	integer, Default: NULL
is_hotspot	logical, TCGA or COSMIC hotspot, Default: NULL
is_damaging	logical, Default: NULL
variant_classification	string, Default: NULL. Select from the following: For DepMap data version prior to 23Q: 3'UTR, 5'Flank, 5'UTR, De_novo_Start_OutOfFrame, Frame_Shift_Del, Frame_Shift_Ins, IGR, In_Frame_Del, In_Frame_Ins, Intron, Missense_Mutation, Nonsense_Mutation, Nonstop_Mutation, Silent, Splice_Site, Start_Codon_Del, Start_Codon_Ins, Start_Codon_SNP, Stop_Codon_Del, Stop_Codon_Ins For DepMap data version 23Q and after: missense_variant, frameshift_variant, splice_acceptor_variant, stop_gained, splice_donor_variant, inframe_deletion, inframe_insertion, stop_lost, start_lost, downstream_gene_variant, protein_altering_variant, 5_prime_UTR_variant, upstream_gene_variant, non_coding_transcript_exon_variant
data_dir	string Path to GRETTA_data

Value

A data frame containing mutations matching criteria of input arguments

Examples

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

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

list_mutations(
gene = 'ARID1A', 
is_damaging = TRUE,
data_dir = gretta_data_dir)

ytakemon/GINIR documentation built on Aug. 2, 2024, 1:32 p.m.