isStructural: Determining whether the variant is a structural variant

In PapenfussLab/StructuralVariantAnnotation: Variant annotations for structural variants

Description

Determining whether the variant is a structural variant

Usage

isStructural(x, ...)

## S4 method for signature 'CollapsedVCF'
isStructural(x, ..., singleAltOnly = TRUE)

## S4 method for signature 'ExpandedVCF'
isStructural(x, ...)

## S4 method for signature 'VCF'
isStructural(x, ...)

Arguments

x	A VCF object.
...	Internal parameters.
singleAltOnly	Whether only single ALT values are accepted. Default is set to TRUE.

Details

The function takes a VCF object as input, and returns a logical value for each row, determining whether the variant is a structural variant.

Value

A logical list of which the length is the same with the input object.

Methods (by class)

• CollapsedVCF: Determining whether a CollapsedVCF object is a strucrual variant. Only single ALT values are accepted.

• ExpandedVCF: Determining whether a ExpandedVCF object is a structural variant.

• VCF: Determining whether a VCF object is a structural variant.

Examples

vcf.file <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation")
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
isStructural(vcf)

PapenfussLab/StructuralVariantAnnotation documentation built on Dec. 25, 2021, 1:20 a.m.