VariantType-class {VariantAnnotation} | R Documentation

## 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,
                           idType=c("gene", "tx"))
        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.
`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.

### 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.

### 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(s)

Valerie Obenchain

### 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

[Package VariantAnnotation version 1.28.13 Index]