addOverallFrequencies-methods: Overall genotypes counts and allele frequencies

In TVTB: TVTB: The VCF Tool Box

Description

Adds dataset-wide genotypes counts (reference homozygote, heterozygote, and alternate homozygote) and allele frequencies (alternate and minor) as INFO fields in an ExpandedVCF object. Counts and frequencies may be calculated across all samples. Multiple genotypes can be counted toward a single frequency (e.g. combined c("0/0", "0|0") for homozygote reference genotypes).

Usage

## S4 method for signature 'ExpandedVCF'
addOverallFrequencies(vcf, force = FALSE)

Arguments

vcf	ExpandedVCF object. metadata(vcf)[["TVTBparam"]] must contain a TVTBparam object.
force	If TRUE, INFO fields header and data are overwritten. If FALSE, an error is thrown if any field already exists.

Details

Genotypes and frequencies are calculated across all the samples in the ExpandedVCF object, and stored in INFO fields named according to settings stored in the TVTBparam object (see below).

The param object controls the key of INFO fields as follows:

names(ref(param))

Count of reference homozygote genotypes.

names(het(param))

Count of heterozygote genotypes.

names(alt(param))

Count of alternate homozygote genotypes.

aaf(param)

Alternate allele frequency.

maf(param)

Minor allele frequency

Value

ExpandedVCF object including additional INFO fields for genotype counts and allele frequencies. See Details.

Warning

A warning message is issued if genotypes are not fully defined in the TVTBparam.

Author(s)

Kevin Rue-Albrecht

See Also

addFrequencies,ExpandedVCF,list-method, addPhenoLevelFrequencies,ExpandedVCF-method, and VCF.

Examples

# Example data ----

# VCF file
vcfFile <- system.file("extdata", "moderate.vcf", package = "TVTB")

# TVTB parameters
tparam <- TVTBparam(Genotypes("0|0", c("0|1", "1|0"), "1|1"))

# Pre-process variants
vcf <- VariantAnnotation::readVcf(vcfFile, param = tparam)
vcf <- VariantAnnotation::expand(vcf, row.names = TRUE)


# Example usage ----

vcf <- addOverallFrequencies(vcf, tparam)

TVTB documentation built on Nov. 8, 2020, 6:09 p.m.