readVcf-methods: Read VCF files

In TVTB: TVTB: The VCF Tool Box

Description

Read Variant Call Format (VCF) files, attaches the given TVTBparam in the metadata slot of the resulting VCF object, and attaches optional phenotype information in the phenoData slot.

Usage

## S4 method for signature 'character,TVTBparam'
readVcf(
    file, genome, param, ..., colData = DataFrame(), autodetectGT = FALSE)
## S4 method for signature 'TabixFile,TVTBparam'
readVcf(
    file, genome, param, ..., colData = DataFrame(), autodetectGT = FALSE)

Arguments

file, genome	See readVcf.
param	TVTBparam object that contains recurrent parameters. The vep slot of param is checked for presence among the INFO keys of the VCF file. The TVTBparam object is coerced to ScanVcfParam using the ranges slot only. All fixed, info, and geno fields are imported (see argument colData to declare samples to import).
...	Additional arguments, passed to methods.
colData	Phenotype information in a DataFrame. If supplied, only samples identifiers present in rownames(colData) are imported from the VCF file. An error is thrown if any of the samples is absent from the VCF file.
autodetectGT	If TRUE, the method updates the genotypes definitions in the TVTBparam object attached to the resulting VCF object after guessing the codes that represent homozygote reference, heterozygote, and homzoygote alternate genotypes.

Value

VCF object. See ?VCF for complete details of the class structure.

Warning

A warning message is issued if genotypes cannot be fully defined, when autodetectGT=TRUE.

Author(s)

Kevin Rue-Albrecht

See Also

readVcf,TabixFile,ScanVcfParam-method, and VCF.

Examples

# Example data ----

# VCF file
vcfFile <- system.file("extdata", "moderate.vcf.gz", 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"))


# Example usage ----

vcf <- readVcf(vcfFile, "b37", tparam, colData = phenotypes)

TVTB documentation built on Nov. 8, 2020, 6:09 p.m.