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\name{VariantType-class}
\docType{class}
% Class
\alias{VariantType-class}
% Subclasses
\alias{CodingVariants-class}
\alias{IntronVariants-class}
\alias{FiveUTRVariants-class}
\alias{ThreeUTRVariants-class}
\alias{SpliceSiteVariants-class}
\alias{IntergenicVariants-class}
\alias{PromoterVariants-class}
\alias{AllVariants-class}
% Constructors for subclasses :
\alias{CodingVariants}
\alias{IntronVariants}
\alias{FiveUTRVariants}
\alias{ThreeUTRVariants}
\alias{SpliceSiteVariants}
\alias{IntergenicVariants}
\alias{PromoterVariants}
\alias{AllVariants}
% accessors :
\alias{upstream}
\alias{upstream,AllVariants-method}
\alias{upstream,PromoterVariants-method}
\alias{upstream,IntergenicVariants-method}
\alias{upstream<-}
\alias{upstream<-,AllVariants-method}
\alias{upstream<-,PromoterVariants-method}
\alias{upstream<-,IntergenicVariants-method}
\alias{downstream}
\alias{downstream,AllVariants-method}
\alias{downstream,PromoterVariants-method}
\alias{downstream,IntergenicVariants-method}
\alias{downstream<-}
\alias{downstream<-,AllVariants-method}
\alias{downstream<-,PromoterVariants-method}
\alias{downstream<-,IntergenicVariants-method}
\alias{promoter}
\alias{promoter,AllVariants-method}
\alias{promoter<-}
\alias{promoter<-,AllVariants-method}
\alias{intergenic}
\alias{intergenic,AllVariants-method}
\alias{intergenic<-}
\alias{intergenic<-,AllVariants-method}
% show method:
\alias{show,VariantType-method}
\alias{show,AllVariants-method}
\alias{show,PromoterVariants-method}
\title{VariantType subclasses}
\description{
\code{VariantType} subclasses specify the type of variant to be located with
\code{locateVariants}.
}
\usage{
CodingVariants()
IntronVariants()
FiveUTRVariants()
ThreeUTRVariants()
SpliceSiteVariants()
IntergenicVariants(upstream = 1e+06L, downstream = 1e+06L)
PromoterVariants(upstream = 2000L, downstream = 200L)
AllVariants(promoter = PromoterVariants(),
intergenic = IntergenicVariants())
}
\details{
\code{VariantType} is a virtual class inherited by the \code{CodingVariants},
\code{IntronVariants}, \code{FiveUTRVariants}, \code{ThreeUTRVariants},
\code{SpliceSiteVariants}, \code{IntergenicVariants} and \code{AllVariants}
subclasses.
The subclasses are used as the \code{region} argument to
\code{locateVariants}. They designate the type of variant (i.e., region of
the annotation to match) when calling \code{locateVariants}.
The majority of subclasses have no slots and require no arguments for an
instance to be created. \code{PromoterVariants} and \code{IntergenicVariants}
and accept \code{upstream} and \code{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 ?\code{locateVariants} man
page for details. \code{AllVariants} accepts \code{promoter} and
\code{intergenic} arguments which are \code{PromoterVariants()} and
\code{IntergenicVariants()} objects with the appropriate
\code{upstream} and \code{downstream} values.
}
\arguments{
\item{upstream, downstream}{
Single \code{integer} values representing the number of base pairs
upstream of the 5'-end and downstream of the 3'-end. Used in contructing
\code{PromoterVariants()} and \code{IntergenicVariants()} objects only.
}
\item{promoter}{
\code{PromoterVariants} object with appropriate \code{upstream} and
\code{downstream} values. Used when constructing \code{AllVariants}
objects only.
}
\item{intergenic}{
\code{IntergenicVariants} object with appropriate \code{upstream} and
\code{downstream} values. Used when constructing \code{AllVariants}
objects only.
}
}
\section{Accessors}{
In the following code, \code{x} is a \code{PromoterVariants} or a
\code{AllVariants} object.
\describe{
\item{}{
\code{upstream(x)}, \code{upstream(x) <- value}:
Gets or sets the number of base pairs defining a range
upstream of the 5' end (excludes 5' start value).
}
\item{}{
\code{downstream(x)}, \code{downstream(x) <- value}:
Gets or sets the number of base pairs defining a range
downstream of the 3' end (excludes 3' end value).
}
\item{}{
\code{promoters(x)}, \code{promoters(x) <- value}:
Gets or sets the \code{PromoterVariants} in the
\code{AllVariants} object.
}
\item{}{
\code{intergenic(x)}, \code{intergenic(x) <- value}:
Gets or sets the \code{IntergenicVariants} in the
\code{AllVariants} object.
}
}
}
\author{Valerie Obenchain <vobencha@fhcrc.org>}
\seealso{
\itemize{
\item The promoters function on the
\link[GenomicRanges]{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
}
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