annotateNearest: 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

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.

Value

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).

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.

Examples

Run this code

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)))

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