determine_double_hit_genes {driveR}

Determine Double-Hit Genes

Description

Determine Double-Hit Genes

Usage

determine_double_hit_genes(
  annovar_csv_path,
  gene_SCNA_df,
  log2_hom_loss_threshold = -1,
  batch_analysis = FALSE
)

Arguments

annovar_csv_path

path to 'ANNOVAR' csv output file

gene_SCNA_df

data frame of gene-level SCNAs (output of create_gene_level_scna_df)

log2_hom_loss_threshold

to determine double-hit events, the log₂ threshold for identifying homozygous loss events (default = -1).

batch_analysis

boolean to indicate whether to perform batch analysis (TRUE, default) or personalized analysis (FALSE). If TRUE, a column named 'tumor_id' should be present in both the ANNOVAR csv and the SCNA table.

Value

vector of gene symbols that are subject to double-hit event(s), i.e. non-synonymous mutation + homozygous copy-number loss