packMatches: Sample packFinder Output

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

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
)

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