packMatches {packFinder} | R Documentation

## Sample packFinder Output

### Description

A sample output from `packSearch` with cluster information. This dataframe is in the format produced by coercing a `link[GenomicRanges:GRanges-class]{GRanges}` object to a dataframe: `data.frame(GRanges)`.

### Usage

    data(packMatches)

### Format

A dataframe of 9 obs. and 7 variables.

### Details

Was obtained from running `packSearch` on the Arabidopsis thaliana chromosome 3 reference sequence, followed by clustering using `packClust`. Contains 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.

The dataset was generated as in the example below.

### See Also

`packSearch`, `data.frame`, `arabidopsisThalianaRefseq`

### Examples

    data(arabidopsisThalianaRefseq)

    packMatches <- packSearch(
        Biostrings::DNAString("CACTACAA"),
        arabidopsisThalianaRefseq,
        elementLength = c(300, 3500),
        tsdLength = 3
    )

[Package packFinder version 1.6.0 Index]