packAlign {packFinder} | R Documentation

## Global Alignment with VSEARCH

### Description

A global pairwise alignment of pack-TYPE elements by sequence similarity. mIt may be useful to run `packClust` to identify groups of similar transposable elements, before generating alignments of each group.

### Usage

    packAlign(
      packMatches,
      Genome,
      identity = 0,
      threads = 1,
      identityDefinition = 2,
      maxWildcards = 0.05,
      saveFolder,
      vSearchPath = "vsearch"
    )

### Arguments

`packMatches` | A dataframe of potential Pack-TYPE transposable elements, in the format given by `packSearch`. This dataframe is in the format produced by coercing a `link[GenomicRanges:GRanges-class]{GRanges}` object to a dataframe: `data.frame(GRanges)`. Will be saved as a FASTA file for VSEARCH.
`Genome` | A DNAStringSet object containing sequences referred to in `packMatches` (the object originally used to predict the transposons `packSearch`).
`identity` | The sequence identity of two transposable elements in `packMatches` required to be grouped into a cluster.
`threads` | The number of threads to be used by VSEARCH.
`identityDefinition` | The pairwise identity definition used by VSEARCH. Defaults to 2, the standard VSEARCH definition.
`maxWildcards` | The maximal allowable proportion of wildcards in the sequence of each match (defaults to `0.05`).
`saveFolder` | The folder to save saveFolder files (uc, blast6out, FASTA)
`vSearchPath` | When the package is run on windows systems, the location of the VSEARCH executable file must be given; this should be left as default on Linux/MacOS systems.

### Value

Saves alignment information, including a `uc`, `blast6out` and a pairwise alignment `fasta` file, to the specified location. Returns the uc summary file generated by the alignment.

### Note

In order to align sequences using VSEARCH, the executable file must first be installed.

### Author(s)

Jack Gisby

### References

VSEARCH may be downloaded from https://github.com/torognes/vsearch, along with a manual documenting the program's parameters. See https://www.ncbi.nlm.nih.gov/pubmed/27781170 for further information.

### See Also

`tirClust`, `packClust`, `readBlast`, `readUc`, `filterWildcards`, `packSearch`

### Examples

    data(arabidopsisThalianaRefseq)
    data(packMatches)

    # packAlign run on a Linux/MacOS system
    ## Not run:
        packAlign(packMatches, Genome)

    ## End(Not run)

    # packAlign run on a Windows system
    ## Not run:
        packAlign(packMatches, Genome,
                vSearchPath = "path/to/vsearch/vsearch.exe")

    ## End(Not run)

[Package packFinder version 1.2.0 Index]