blastAnnotate: Functional Annotation of PackTYPE Elements
In jackgisby/packFinder: de novo Annotation of Pack-TYPE Transposable Elements

blastAnnotate

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).

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)

jackgisby/packFinder documentation built on July 19, 2022, 2:25 a.m.