blastAnnotate {packFinder} | R Documentation

## Functional Annotation of PackTYPE Elements

### Description

Uses hits, previously generated using blast, to annotate transposon hits. Transposons with non-redundant transposase hits are classed as autonomous ("auto"), while others are classed as "other" or "pack" based on whether the element has non-redundant hits to other proteins.

### Usage

    blastAnnotate(protHits, autoHits, packMatches)

### Arguments

`protHits` | BLAST results for non-transposon related genes or proteins (as a `data.frame`). Generated using `blastAnalysis`.
`autoHits` | BLAST results for transposon related genes or proteins (as a `data.frame`). Generated using `blastAnalysis`.
`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.

### Value

Returns the original `packMatches` dataframe, with the addition of a "classification" column containing one of the following values:

- auto - elements that match known transposases or transposon-related proteins are classified as autonomous elements

- pack - elements that match other proteins or genic sequences may be classified as Pack-TYPE elements

- other - elements that generate no significant hits

### Note

Requires that the query ids in the protein and autonomous hits match the row names in packMatches.

### Author(s)

Jack Gisby

### References

For further information, see the NCBI BLAST+ application documentation and help pages (https://www.ncbi.nlm.nih.gov/pubmed/20003500?dopt=Citation).

### See Also

`blastAnalysis`, `readBlast`, `packBlast`

### Examples

    data("packMatches")

    # read in some protein hits
    p <- data.frame(
        query_id = c(2, 3),
        subject_id = c("prot", "hyp")
    )

    # read in some autonomous hits
    a <- data.frame(
        query_id = c(3, 4),
        subject_id = c("transposase", "mutator")
    )

    blastAnnotate(p, a, packMatches)

[Package packFinder version 1.4.0 Index]