ReadVEP: Read a VEP tsv file

In nbroguiere/burgertools: Collection of tools extending the functionality of Seurat

Read a VEP tsv file

Description

This function reads a variant effect predictor (VEP) output file in tsv format, and returns the contents as a tibble.

Usage

ReadVEP(file, remove_empty_col = TRUE)

Arguments

file	character(1) The path to the VEP file, can be compressed (.vcf or .vcf.gz).
remove_empty_col	logical(1) Should uninformative columns with only a unique value/level be removed. Default: TRUE.

Details

This function is a readr::read_tsv wrapper that reads a variant effect predictor (VEP) output file in tsv format, and returns the contents as a tibble. By default, removes uninformative columns (i.e. which have only one value), and setups the IMPACT (if present) as an ordered factor.

Value

A tibble

Examples

genotypes <- ReadVEP("MyFolder/MyVEPresults.tsv.gz")

nbroguiere/burgertools documentation built on Jan. 30, 2024, 3:48 a.m.