annotateNearest {bumphunter} | R Documentation

## Annotate the results of nearest

### Description

Annotate the results of nearest with more information about the type of match.

### Usage

    annotateNearest(x, subject, annotate = TRUE, ...)

### Arguments

`x` | The query. An `IRanges` or `GenomicRanges` object, or a `data.frame` with columns for `start`, `end`, and, optionally, `chr` or `seqnames`.
`subject` | The subject. An `IRanges` or `GenomicRanges` object, or a `data.frame` with columns for `start`, `end`, and, optionally, `chr` or `seqnames`.
`annotate` | Whether to annotate the result.
`...` | Arguments passed along to `nearest`.

### Details

This function runs `nearest` and then annotates the nearest hit. Note that the nearest subject range to a given query may not be unique and we arbitrarily chose one as done by default by `nearest`.

### Value

A data frame with columns `c("distance", "subjectHits", "type", "amountOverlap", "insideDistamce", "size1", "size2")` unless `annotate` is `FALSE`, in which case only the first two columns are returned as an integer matrix.

`dist` | Signed distance to the nearest target. Queries downstream from (i.e. past) their nearest target are given a negative distance.
`subjectHits` | The index of the nearest target.
`type` | one of `c("inside", "cover", "disjoint", "overlap")`.
`amountOverlap` | The width of the overlap region, if any.
`insideDistance` | When a query is contained in its nearest target, the signed minimum of the two distances target-start-to-query-start and query-end-to-target-end. The former is taken positive, and the latter, which wins in ties, negative. `dist` will be `0` in this case.
`size1` | equals `width(x)`.
`size2` | equals `width(subject)`.

### Author(s)

Harris Jaffee, Peter Murakami and Rafael A. Irizarry

### See Also

`nearest`, `matchGenes`

### Examples

    query <- GRanges(seqnames = 'chr1', IRanges(c(1, 4, 9), c(5, 7, 10)))
    subject <- GRanges('chr1', IRanges(c(2, 2, 10), c(2, 3, 12)))
    nearest(query, subject)
    distanceToNearest(query, subject)

    ## showing 'cover' and 'disjoint', and 'amountOverlap'
    annotateNearest(query, subject)

    ## showing 'inside' and 'insideDist', and 'amountOverlap'
    annotateNearest(subject, query)
    annotateNearest(GRanges('chr1', IRanges(3,3)), GRanges('chr1', IRanges(2,5)))
    annotateNearest(GRanges('chr1', IRanges(3,4)), GRanges('chr1', IRanges(2,5)))
    annotateNearest(GRanges('chr1', IRanges(4,4)), GRanges('chr1', IRanges(2,5)))

[Package bumphunter version 1.28.0 Index]