Description Usage Arguments Details Accessors Author(s) See Also Examples
VariantType
subclasses specify the type of variant to be located with
locateVariants
.
1 2 3 4 5 6 7 8 9 10 | 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())
|
upstream, downstream |
Single |
idType |
|
promoter |
|
intergenic |
|
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.
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.
Valerie Obenchain
The promoters function on the intra-range-methods man page in the GenomicRanges package.
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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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