tirClust {packFinder} | R Documentation

## Analyse TIR Sequences of Pre-clustered Transposable Elements

### Description

Takes transposable elements clustered by VSEARCH, `packClust`, and produces consensus sequences for the terminal inverted repeats of each. Allows for the visualisation of TIR similarities between clusters for both forward and reverse strands.

### Usage

    tirClust(
      packMatches,
      Genome,
      tirLength = 25,
      plot = TRUE,
      plotSavePath = NULL,
      k = 5,
      output = "consensus"
    )

### Arguments

`packMatches` | A dataframe containing genomic ranges and names referring to sequences to be extracted. This dataframe is in the format produced by coercing a `link[GenomicRanges:GRanges-class]{GRanges}` object to a dataframe: `data.frame(GRanges)`. 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.
`Genome` | A DNAStringSet object containing sequences referred to in `packMatches` (the object originally used to predict the transposons `packSearch`).
`tirLength` | The TIR size to be considered. Consensus sequences will be generated based on the first and last `tirLength` bases of a transposon.
`plot` | Argument specifying whether the TIR consensus sequences should be plottted as a dendrogram.
`plotSavePath` | File path for the dendrogram plot. If unspecified, the dendrogram plot is not saved.
`k` | The k-mer size to be used for calculating a distance matrix between TIR consensus sequences. See `kdistance`. Larger word sizes will not be suitable for longer TIR sequences, due to processing time required. Additionally, k must be greater than the TIR sequence length.
`output` | Controls the output of `tirClust`. If output is specified as "consensus", the consensus sequences of each TIR cluster will be returned; else, if output is specified as "dendrogram", a dendrogram object will be returned for creation of customisable plots.

### Value

If `output` is specified as "consensus" (default), returns a list of consensus sequences for each cluster specified in `packMatches` as a `DNAStringSet`. Else if `output` is specified as "dendrogram", returns a dendrogram object used to create hierarchical clustering diagrams.

### Author(s)

Jack Gisby

### See Also

codepackClust, codepackAlign, `kdistance`, `DNAStringSet`, `as.alignment`, `packSearch`

### Examples

    data(arabidopsisThalianaRefseq)
    data(packMatches)

    tirClust(packMatches, arabidopsisThalianaRefseq)

[Package packFinder version 1.0.0 Index]