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 |
upstream, downstream |
Single |
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.
Robert Castelo <robert.castelo@upf.edu>
The VariantType-class man page in the
VariantAnnotation
package.
1 2 |
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