VariantType subclasses

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,
                       idType=c("gene", "tx"))
    PromoterVariants(upstream = 2000L, downstream = 200L)
    AllVariants(promoter = PromoterVariants(),
                intergenic = IntergenicVariants())

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. IntergenicVariants also accepts a idType that controls what IDs are returned in the PRECEDEID and FOLLOWID metadata columns.

AllVariants accepts promoter and intergenic arguments which are PromoterVariants() and IntergenicVariants() objects with the appropriate upstream and downstream values.

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.

idType

character indicating if the ids in the PRECEDEID and FOLLOWID metadata columns should be gene ids ("gene") or transcript ids ("tx"). Applicable to 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).

idType(x), idType(x) <- value

Gets or sets the character() which controls the id returned in the PRECEDEID and FOLLOWID output columns. Possible values are "gene" and "tx".

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.

Author

Valerie Obenchain

See also

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

Examples

  CodingVariants()
#> class: CodingVariants 
  SpliceSiteVariants()
#> class: SpliceSiteVariants 
  PromoterVariants(upstream=1000, downstream=10000)
#> class: PromoterVariants 
#> upstream: 1000 
#> downstream: 10000 

  ## Default values for PromoterVariants and IntergenicVariants
  AllVariants()
#> class: AllVariants 
#> promoter: 
#>   upstream: 2000 
#>   downstream: 200 
#> intergenic: 
#>   upstream: 1000000 
#>   downstream: 1000000 
#>   idType: gene 
  ## Modify 'upstream' and 'downstream' for IntergenicVariants
  AllVariants(intergenic=IntergenicVariants(500, 100))
#> class: AllVariants 
#> promoter: 
#>   upstream: 2000 
#>   downstream: 200 
#> intergenic: 
#>   upstream: 500 
#>   downstream: 100 
#>   idType: gene 
  ## Reset PromoterVariants on existing AllVariants object
  av <- AllVariants()
  av
#> class: AllVariants 
#> promoter: 
#>   upstream: 2000 
#>   downstream: 200 
#> intergenic: 
#>   upstream: 1000000 
#>   downstream: 1000000 
#>   idType: gene 
  promoter(av) <- PromoterVariants(100, 50)
  av
#> class: AllVariants 
#> promoter: 
#>   upstream: 100 
#>   downstream: 50 
#> intergenic: 
#>   upstream: 1000000 
#>   downstream: 1000000 
#>   idType: gene