VariantAnnotation (version 1.18.5)

VariantType-class: VariantType subclasses

Description

VariantType subclasses specify the type of variant to be located with locateVariants.

Usage

CodingVariants() IntronVariants() FiveUTRVariants() ThreeUTRVariants() SpliceSiteVariants() IntergenicVariants(upstream = 1e+06L, downstream = 1e+06L) PromoterVariants(upstream = 2000L, downstream = 200L) AllVariants(promoter = PromoterVariants(), intergenic = IntergenicVariants())

Arguments

upstream, downstream

Single integer values representing the number of base pairs upstream of the 5'-end and downstream of the 3'-end. Used in contructing PromoterVariants() and IntergenicVariants() objects only.

promoter

PromoterVariants object with appropriate upstream and downstream values. Used when constructing AllVariants objects only.

intergenic

IntergenicVariants object with appropriate upstream and downstream values. Used when constructing AllVariants objects only.

Accessors

In the following code, x is a PromoterVariants or a AllVariants object.

upstream(x), upstream(x) <- value: Gets or sets the number of base pairs defining a range upstream of the 5' end (excludes 5' start value).

downstream(x), downstream(x) <- value: Gets or sets the number of base pairs defining a range downstream of the 3' end (excludes 3' end value).

promoters(x), promoters(x) <- value: Gets or sets the PromoterVariants in the AllVariants object.

intergenic(x), intergenic(x) <- value: Gets or sets the IntergenicVariants in the AllVariants object.

Details

VariantType is a virtual class inherited by the CodingVariants, IntronVariants, FiveUTRVariants, ThreeUTRVariants, SpliceSiteVariants, IntergenicVariants and AllVariants subclasses.

The subclasses are used as the region argument to locateVariants. They designate the type of variant (i.e., region of the annotation to match) when calling locateVariants.

The majority of subclasses have no slots and require no arguments for an instance to be created. PromoterVariants and IntergenicVariants and accept upstream and downstream arguments that define the number of base pairs upstream from the 5'-end and downstream from the 3'-end of the transcript region. See the ?locateVariants man page for details. AllVariants accepts promoter and intergenic arguments which are PromoterVariants() and IntergenicVariants() objects with the appropriate upstream and downstream values.

See Also

• The promoters function on the intra-range-methods man page in the GenomicRanges package.

Examples

  CodingVariants()
  SpliceSiteVariants()
  PromoterVariants(upstream=1000, downstream=10000)

  ## Default values for PromoterVariants and IntergenicVariants
  AllVariants()
  ## Modify 'upstream' and 'downstream' for IntergenicVariants
  AllVariants(intergenic=IntergenicVariants(500, 100))
  ## Reset PromoterVariants on existing AllVariants object
  av <- AllVariants()
  av
  promoter(av) <- PromoterVariants(100, 50)
  av