Load data from a VCF file — load

This function parses a set of mutations in the Variant Calling Format (VCF), using the vcfR R package. The function takes in input the column names of the INFO field referring to allele depth counts, and number of reads with the variant. The two columns are used to compute the variant allele frequency (VAF) value; if any of the required columns are not found, an error is returned. This function does not filter any of the variants annotated in the input VCF file.

Usage

load_vcf(file, DP_column = "DP", NV_column = "NV")

Arguments

file: A VCF file name.
DP_column: Column with the total depth (DP), i.e., sum of reads at a locus.
NV_column: Column with the number of reads with the variant (NV).

Value

A tibble with the loaded data which contains, besides all the content parsable from the VCF file, three columns named DP, NV and VAF where VAF = NV/DP.

Examples

# Example VCF file in the https://github.com/openvax/varcode repository
file = 'https://raw.githubusercontent.com/openvax/varcode/master/test/data/strelka-example.vcf'

download.file(url = file, destfile = 'strelka-example.vcf')
#> Warning: downloaded length 0 != reported length 14
#> Warning: cannot open URL 'https://raw.githubusercontent.com/openvax/varcode/master/test/data/strelka-example.vcf': HTTP status was '404 Not Found'
#> Error in download.file(url = file, destfile = "strelka-example.vcf"): cannot open URL 'https://raw.githubusercontent.com/openvax/varcode/master/test/data/strelka-example.vcf'

# We pretend that the number of variants is the gt_DP2 field, which is wrong
# Anyway, this shows how you can load a VCF file.
load_vcf(file = 'strelka-example.vcf', DP_column = 'gt_DP', NV_column = 'gt_DP2')
#> Error in load_vcf(file = "strelka-example.vcf", DP_column = "gt_DP", NV_column = "gt_DP2"): Input file not found: strelka-example.vcf