getPacksFromGRanges: Retrieve packFinder Results from GRanges Object
In packFinder: de novo Annotation of Pack-TYPE Transposable Elements
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
View source: R/getPacksFromGRanges.R
Description
A link[GenomicRanges:GRanges-class]{GRanges}
object, potentially
generated using packSearch and
packsToGRanges, can be converted to a
dataframe. If a GRanges object is supplied without TSD
information, this can be calculated and appended to the
final dataframe.
Usage
1
getPacksFromGRanges(packGRanges, Genome = NULL, tsdLength = NULL)
Arguments
packGRanges
link[GenomicRanges:GRanges-class]{GRanges}
object to be coerced.
Genome
(optional) Sequences referred to by packGRanges.
tsdLength
(optional) Length of TSD sequences.
Value
Dataframe in the format used by packSearch.
If Genome and tsdLength are supplied, then
TSD sequences are retrieved and returned
as part of the dataframe.
Author(s)
Jack Gisby
See Also
packsToGRanges,
link[GenomicRanges:GRanges-class]{GRanges},
packSearch
Examples
1
2
3
4
data(packMatches)
GRangesObject <- packsToGRanges(packMatches)
packMatches <- getPacksFromGRanges(GRangesObject)
packFinder documentation built on Nov. 8, 2020, 5:24 p.m.
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Description Usage Arguments Value Author(s) See Also Examples
View source: R/getPacksFromGRanges.R
Description
A link[GenomicRanges:GRanges-class]{GRanges}
object, potentially
generated using packSearch and
packsToGRanges, can be converted to a
dataframe. If a GRanges object is supplied without TSD
information, this can be calculated and appended to the
final dataframe.
Usage
1 | getPacksFromGRanges(packGRanges, Genome = NULL, tsdLength = NULL)
|
Arguments
packGRanges |
|
Genome |
(optional) Sequences referred to by |
tsdLength |
(optional) Length of TSD sequences. |
Value
Dataframe in the format used by packSearch.
If Genome and tsdLength are supplied, then
TSD sequences are retrieved and returned
as part of the dataframe.
Author(s)
Jack Gisby
See Also
packsToGRanges,
link[GenomicRanges:GRanges-class]{GRanges},
packSearch
Examples
1 2 3 4 | data(packMatches)
GRangesObject <- packsToGRanges(packMatches)
packMatches <- getPacksFromGRanges(GRangesObject)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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