countGenos-methods: Count occurences of genotypes
In kevinrue/TVTB: TVTB: The VCF Tool Box

Description Usage Arguments Value Author(s) See Also Examples

Counts the total occurences of a set of genotypes by row in a matrix of genotype. 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.

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## S4 method for signature 'ExpandedVCF'
countGenos(
    x, genos, pheno = NULL, level = NULL)

`x`	`ExpandedVCF` object.
`genos`	`character` vector of genotypes to count (toward a common unique total).
`pheno`	If `x` is an `ExpandedVCF` object, phenotype in `colnames(colData(x))`.
`level`	If `x` is an `ExpandedVCF` object, phenotype level in `colData(x)[,pheno]`.

An integer vector representing the aggregated count of the given genotypes in each row.

Kevin Rue-Albrecht

VCF

# 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 <- countGenos(vcf, het(tparam), "super_pop", "AFR")