driveR (version 0.4.1)

predict_coding_impact: Create Coding Impact Meta-prediction Score Data Frame

Description

Create Coding Impact Meta-prediction Score Data Frame

Usage

predict_coding_impact(
  annovar_csv_path,
  keep_highest_score = TRUE,
  keep_single_symbol = TRUE,
  na.string = "."
)

Value

data frame of meta-prediction scores containing 2 columns:

gene_symbol

HGNC gene symbol

metaprediction_score

metapredictor impact score

Arguments

annovar_csv_path

path to 'ANNOVAR' csv output file

keep_highest_score

boolean to indicate whether to keep only the maximal impact score per gene (default = TRUE). If FALSE, all scores per each gene are returned

keep_single_symbol

in ANNOVAR outputs, a variant may be annotated as exonic in multiple genes. This boolean argument controls whether or not to keep only the first encountered symbol for a variant (default = TRUE)

na.string

string that was used to indicate when a score is not available during annotation with ANNOVAR (default = ".")

Examples

path2annovar_csv <- system.file("extdata/example.hg19_multianno.csv",
                                package = "driveR")
metapred_df <- predict_coding_impact(path2annovar_csv)