packsToGRanges {packFinder} | R Documentation

## 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)

[Package packFinder version 1.4.0 Index]