isStructural {StructuralVariantAnnotation} | R Documentation |
Determining whether the variant is a structural variant
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, ...)
x |
A VCF object. |
... |
Internal parameters. |
singleAltOnly |
Whether only single ALT values are accepted. Default is set to TRUE. |
The function takes a VCF object as input, and returns a logical value for each row, determining whether the variant is a structural variant.
A logical list of which the length is the same with the input object.
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.
vcf.file <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation") vcf <- VariantAnnotation::readVcf(vcf.file, "hg19") isStructural(vcf)