addFrequencies-methods: Group-level genotypes counts and allele frequencies

In kevinrue/TVTB: TVTB: The VCF Tool Box

Description

Adds 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 overall (i.e. across all samples), or within groups of samples (i.e. within phenotype levels). 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,list'
addFrequencies(vcf, phenos, force = FALSE)

## S4 method for signature 'ExpandedVCF,character'
addFrequencies(vcf, phenos, force = FALSE)

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

Arguments

vcf	ExpandedVCF object. metadata(vcf)[["TVTBparam"]] must contain a TVTBparam object.
phenos	If NULL, counts and frequencies are calculated across all samples. Otherwise, either a character vector of phenotypes in colnames(colData(vcf)), or a named list in which names are phenotypes in colnames(colData(vcf)) and values are character vectors of phenotype levels in colData(vcf)[,phenotype]. See Details below.
force	If TRUE, INFO fields header and data are overwritten with a message, if present. If FALSE, an error is thrown if any field already exists.

Details

The phenos argument is central to control the behaviour of this method.

If phenos=NULL, 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).

If phenos is a character vector of phenotypes present in colnames(colData(vcf)), counts and frequencies are calculated for each level of those phenotypes, and stored in INFO fields prefixed with "<phenotype>_<level>_" and suffixed with the settings stored in the param object (see below).

Finally, if phenos is a named list, names must be phenotypes present in colnames(colData(vcf)), and values must be levels of those phenotypes. In this case, counts and frequencies are calculated for the given levels of the given phenotypes, and stored in INFO fields as described above.

The param 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.

Author(s)

Kevin Rue-Albrecht

See Also

addOverallFrequencies,ExpandedVCF-method, addPhenoLevelFrequencies,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 <- addFrequencies(vcf, list(super_pop = "AFR"))

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