getPacksFromGRanges: Retrieve packFinder Results from GRanges Object

In jackgisby/packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Retrieve packFinder Results from GRanges Object

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

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

data(packMatches)

GRangesObject <- packsToGRanges(packMatches)
packMatches <- getPacksFromGRanges(GRangesObject)

jackgisby/packFinder documentation built on July 19, 2022, 2:25 a.m.