packsToGRanges: Export packFinder Results to a GRanges Object

Description Usage Arguments Value Author(s) See Also Examples

View source: R/packsToGRanges.R

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

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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

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packFinder documentation built on Nov. 8, 2020, 5:24 p.m.