addPhenoLevelFrequencies-methods: Genotypes and allele frequencies for a given phenotype level

In kevinrue/TVTB: TVTB: The VCF Tool Box

Description

Adds genotypes counts (reference homozygote, heterozygote, and alternate homozygote) and allele frequencies (alternate and minor) calculated in a group of samples associated with a given level of a given phenotype as INFO fields in an ExpandedVCF object. 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'
addPhenoLevelFrequencies(
    vcf, pheno, level, force = FALSE)

Arguments

vcf	ExpandedVCF object. metadata(vcf)[["TVTBparam"]] must contain a TVTBparam object.
pheno	Phenotype in colnames(colData(vcf)).
level	Phenotype level in colData(vcf)[,pheno].
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 within the groups of samples associated with the given level of the given phenotype, and stored in INFO fields named according to settings stored in metadata(vcf)[["TVTBparam"]] (see below).

The TVTBparam object controls the key suffix 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, addOverallFrequencies,ExpandedVCF-method, VCF, and TVTBparam.

Examples

# Example data ----

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

# Phenotype file
phenoFile <- system.file("extdata", "moderate_pheno.txt", package = "TVTB")
phenotypes <- S4Vectors::DataFrame(read.table(phenoFile, TRUE, row.names = 1))

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

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


# Example usage ----

vcf <- addPhenoLevelFrequencies(vcf, "super_pop", "AFR")

kevinrue/TVTB documentation built on Sept. 6, 2021, 10:52 p.m.