SimpleReadVCF: Read a VCF file into a data frame with minimal processing.
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

View source: R/VCF_to_catalog_functions.R

SimpleReadVCF

R Documentation

Read a VCF file into a data frame with minimal processing.

Description

Read a VCF file into a data frame with minimal processing.

Usage

SimpleReadVCF(file)

Arguments

file

The name/path of the VCF file, or a complete URL.

Details

Header lines beginning "##" are removed, and column "#CHROM" is renamed to "CHROM". Other column names are unchanged. Columns "#CHROM", "POS", "REF", and "ALT" must be in the input.

Value

A data frame storing mutation records of a VCF file.

Examples

file <- c(system.file("extdata/Strelka-SBS-vcf",
                      "Strelka.SBS.GRCh37.s1.vcf",
                      package = "ICAMS"))
df <- SimpleReadVCF(file)

ICAMS documentation built on June 15, 2025, 1:08 a.m.