addCountGenos-methods: Add count of genotypes to INFO field
In kevinrue/TVTB: TVTB: The VCF Tool Box

Description Usage Arguments Details Value Author(s) See Also Examples

Adds the total occurences of a set of genotypes as an INFO field for each variant. All given genotypes are counted toward a single total (e.g. grand total of c("0/0", "0|0")), while other genotypes are silently ignored.

## S4 method for signature 'ExpandedVCF'
addCountGenos(
        vcf, genos, key, description,
        samples = 1:ncol(vcf), force = FALSE)

`vcf`	`ExpandedVCF` object.
`genos`	`character` vector of genotypes to count (toward a common unique total).
`key`	Name of the INFO field to create or update (`character` vector of length 1). See Details below.
`description`	`character` description of the INFO field to create or overwrite (`character` vector of length 1).
`samples`	`integer`, `numeric` or `character` vector indicating samples to consider in `VariantAnnotation::geno(vcf)`. If not specified, all samples are considered.
`force`	If `TRUE`, the field header and data will be overwritten if present; If `FALSE`, an error is thrown if the field already exists.

In all cases, the new INFO field is inserted after the last existing field. In other words, overwriting an existing INFO field is achieved by dropping it from the data and header of the info slot, and subsequently inserting the new data after the last remaining INFO field.

ExpandedVCF object including an additional INFO field stating the count of genotypes.

Kevin Rue-Albrecht

countGenos,ExpandedVCF-method and geno,VCF-method

# Example data ----

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

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

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


# Example usage ----

vcf <- addCountGenos(
    vcf, het(tparam),
    suffix(tparam)["het"],
    "Number of heterozygous genotypes")