vepInPhenoLevel-methods: VEP predictions of variants observed in samples

In kevinrue/TVTB: TVTB: The VCF Tool Box

VEP predictions of variants observed in samples

Description

Returns VEP predictions for variants observed (uniquey) in samples associated with a given phenotype level.

Usage

## S4 method for signature 'ExpandedVCF'
vepInPhenoLevel(
    vcf, phenoCol, level, vepCol, unique = FALSE)

Arguments

vcf	ExpandedVCF object. metadata(vcf)[["TVTBparam"]] must contain a TVTBparam object.
phenoCol	Name of a column in pheno.
level	Phenotype level; only variants observed in at least one sample will be considered.
vepCol	VEP prediction fields; character vector of metadata columns in parseCSQToGRanges(vcf).
unique	If TRUE, consider only variants unique to the phenotype level (i.e. absent from all other phenotype levels).

Value

A GRanges including all VEP predictions associated with a variant seen in at least one sample (heterozygote or alternate homozygote) associated with the phenotype level. The GRanges contains at least one column for the VEP prediction value. Additional columns containing another VEP prediction field may be added using the facet argument.

Note

If available, "Feature" is a recommended value for this argument, as VEP typically produce one prediction per variant per feature.

Warning

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

Author(s)

Kevin Rue-Albrecht

See Also

VCF, GRanges, and DataFrame.

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 ----

vepInPhenoLevel(vcf, "super_pop", "AFR", c("CADD_PHRED", "Feature", "IMPACT"))

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