Nearest Subject Range per Query — fast

Compute nearest-neighbor mapping from query ranges to subject ranges.

Usage

fast_nearest(
  query,
  subject,
  ignore_strand = FALSE,
  threads = fast_default_threads()
)

Arguments

query: An IRanges or GRanges query object.
subject: An IRanges or GRanges subject object.
ignore_strand: Logical scalar. Ignored for non-genomic ranges.
threads: Integer scalar thread count. Included for API consistency.

Value

A S4Vectors::DataFrame with query_id, subject_id, and distance columns.

Details

These functions answer nearest-neighbor questions rather than overlap questions.

fast_nearest() and fast_distance_to_nearest() return one row per matched query.

query_id is the row index in query.

subject_id is the row index of the nearest subject.

distance is 0 when the query overlaps the subject and positive when the nearest subject is separated by a gap.

Examples

q <- IRanges::IRanges(start = c(1, 10, 20), width = c(5, 4, 3))
s <- IRanges::IRanges(start = c(3, 9, 18), width = c(4, 6, 5))
fast_nearest(q, s)
#> DataFrame with 3 rows and 3 columns
#>    query_id subject_id  distance
#>   <integer>  <integer> <integer>
#> 1         1          1         0
#> 2         2          2         0
#> 3         3          3         0