VariantType subclasses specify the type of variant to be located with
locateVariants() from the
VariantAnnotation package. Here we describe two such subclasses defined
ThreeSpliceSiteVariants. For further details on the
VariantType-class please consult the corresponding
manual page in the
FiveSpliceSiteVariants(minIntronLength=20L, upstream = 3L, downstream = 4L) ThreeSpliceSiteVariants(minIntronLength=20L, upstream = 18L, downstream = 3L)
Minimum intron length in nucleotides, by default
can be used as in the
region argument to the
locateVariants() function from the
package or as values in the
regionAnnotations argument to the
VariantFilteringParam() function that constructs a
VariantFilteringParam-class object. These two subclasses allow
VariantFiltering and the function
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
In the following code,
x is a
PromoterVariants or a
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) <- 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) <- 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.
Robert Castelo <email@example.com>
The VariantType-class man page in the
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