parse_annovar_mutation: Parse ANNOVAR mutation

In jhrcook/KrasAlleleCna: The Allele-Specific CNA Analysis of KRAS in CRC

Description

Reads and parses an ANNOVAR file to return the amino acid change in a more understandable way in the column named aa_mod.

Usage

parse_annovar_mutation(anno_tib)

Arguments

anno_tib

tibble of the ANNOVAR file

Value

Returns the tibble, checking if it is empty. If the file was empty, an empty tibble is returned. A column is added that has a simple version of the amino acid change aa_mod.

Examples

extdata_dir <- system.file("extdata", package = "KrasAlleleCna")
annovar_file <- readRDS(file.path(extdata_dir, "annovar_output_list.rds"))[[3]]
annovar_file

parsed_annovar <- parse_annovar_mutation(annovar_file)
parsed_annovar

# the new column has easy to use amino acid mutations
parsed_annovar$aa_mod

jhrcook/KrasAlleleCna documentation built on May 28, 2019, 1:22 p.m.