variantsInSamples-methods: Identify variants observed in samples

In kevinrue/TVTB: TVTB: The VCF Tool Box

Identify variants observed in samples

Description

Identifies variants observed (uniquely) in at least one sample of a given group.

Usage

## S4 method for signature 'ExpandedVCF'
variantsInSamples(
    vcf, samples = 1:ncol(vcf), unique = FALSE)

Arguments

vcf	ExpandedVCF object. metadata(vcf)[["TVTBparam"]] must contain a TVTBparam object.
samples	integer, numeric or character vector indicating samples to consider in VariantAnnotation::geno(vcf). If not specified, all samples are considered.
unique	If TRUE, consider only variants unique to the phenotype level (i.e. not seen in any other phenotype level).

Value

An named integer vector of indices indicating the name and index of variants that are (uniquely) observed in at least one non-reference genotype in the given group of samples.

Warning

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

Author(s)

Kevin Rue-Albrecht

See Also

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(file = phenoFile, header = 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 ----

variantsInSamples(
    vcf,
    which(SummarizedExperiment::colData(vcf)[,"super_pop"] == "EUR"))

kevinrue/TVTB documentation built on July 9, 2024, 11:42 p.m.