packsToGRanges: Export packFinder Results to a GRanges Object

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

Export packFinder Results to a GRanges Object

Description

A dataframe containing genomic ranges and names referring to sequences to be extracted, likely obtained from packSearch, can be converted to a GRanges object. Can be converted back to a dataframe using getPacksFromGRanges. Additional features, such as clusters and TSD sequences, will be included in the object as metadata columns.

Usage

packsToGRanges(packMatches)

Arguments

packMatches

A dataframe containing genomic ranges and names referring to sequences to be extracted. Can be obtained from packSearch or generated from a GRanges object, after conversion to a dataframe. Must contain the following features: start - the predicted element's start base sequence position. end - the predicted element's end base sequence position. seqnames - character string referring to the sequence name in Genome to which start and end refer to.

Value

A GRanges object containing the ranges contained in packMatches and additional metadata columns. May be easily converted between dataframe and GRanges format for use in the packFinder package and link[GenomicRanges:GRanges-class]{GRanges} package. Note that most functions in the packFinder package require sequence ranges to be provided in dataframe format.

Author(s)

Jack Gisby

See Also

getPacksFromGRanges, link[GenomicRanges:GRanges-class]{GRanges}

Examples

data(packMatches)
packGRanges <- packsToGRanges(packMatches)

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