VariantType-class: FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses...
In VariantFiltering: Filtering of coding and non-coding genetic variants

Description Usage Arguments Details Accessors Author(s) See Also Examples

VariantType subclasses specify the type of variant to be located with the function locateVariants() from the VariantAnnotation package. Here we describe two such subclasses defined within the VariantFiltering package: FiveSpliceSiteVariants and ThreeSpliceSiteVariants. For further details on the VariantType-class please consult the corresponding manual page in the VariantAnnotation package.

1 2	FiveSpliceSiteVariants(minIntronLength=20L, upstream = 3L, downstream = 4L) ThreeSpliceSiteVariants(minIntronLength=20L, upstream = 18L, downstream = 3L)

minIntronLength

Minimum intron length in nucleotides, by default minIntronLength=20L. Splice sites annotated within introns smaller than this length will not be used to annotate variants.

upstream, downstream

Single integer values representing the number of nucleotides upstream and downstream of the 5' and 3' dinucleotide ends of introns. By default, the constructor function FiveSpliceSiteVariants has values upstream=3L and downstream=4L, corresponding to 3 nucleotides upstream and 4 nucleotides downstream of the first dinucleotide of the intron, while ThreeSpliceSiteVariants has values upstream=18L and downstream=3L, corresponding to 18 nucleotides upstream and 4 nucleotides downstream of the last dinucleotide of the intron.

The subclasses FiveSpliceSiteVariants and ThreeSpliceSiteVariants can be used as in the region argument to the locateVariants() function from the VariantAnnotation package or as values in the regionAnnotations argument to the VariantFilteringParam() function that constructs a VariantFilteringParam-class object. These two subclasses allow the package VariantFiltering and the function locateVariants() in the VariantAnnotation package, to annotate variants located within a splice site region defined by the user. The boundaries of this region as well as the minimum intron length can be defined with the following arguments to the constructor functions:

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

: minIntronLength(x), minIntronLength(x) <- value: Gets or sets the minimum number of nucleotides long of introns to be considered in the annotation of splice sites.
: upstream(x), upstream(x) <- value: Gets or sets the number of nucleotides upstream of the 5' and 3' end of the intron, excluding the first and last dinucleotide, respectively.
: downstream(x), downstream(x) <- value: Gets or sets the number of nucleotides downstream of the 5' and 3' end of the intron, excluding the first and last dinucleotide, respectively.