distance_to_nearest-methods: Distance in bases to the closest interval(s)

In genomeIntervals: Operations on genomic intervals

Description

Given two objects, from and to, compute the distance in bases of each from interval to the nearest to interval(s). The distance between a base and the next inter-bases on either side values 0.5. Thus, base - base and inter-base - inter-base intervals distances are integer, whereas base - inter-base intervals distances are half-integers.

Usage

## S4 method for signature 'Genome_intervals,Genome_intervals'
distance_to_nearest(from, to)
## S4 method for signature 
## 'Genome_intervals_stranded,Genome_intervals_stranded'
distance_to_nearest(from, to)

Arguments

from	A Genome_intervals or Genome_intervals_stranded object.
to	A Genome_intervals or Genome_intervals object.

Details

A wrapper calling intervals::distance_to_nearest by seqnames and by strand (if both from and to are Genome_intervals_stranded objects). Thus, if both are stranded, distances are computed over each strand separately. One object must be coerced to Genome_intervals if this is not wished.

Value

A numeric vector of distances with one element for each row of from.

See Also

intervals::distance_to_nearest

Examples

## load toy examples
data(gen_ints)

## i in close_intervals notation
close_intervals(i)

## j in close_intervals notation
close_intervals(j)

## distances from i to j
dn = distance_to_nearest(i,j)
dn

## distance == 0 if and only if the interval overlaps another one:
io = interval_overlap(i,j)
if( any( ( sapply(io, length) >0 )  != (!is.na(dn) & dn ==0) ) )
 	stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.")

## distances without strand-specificity
distance_to_nearest(
 		as(i,"Genome_intervals"),
 		as(j,"Genome_intervals")
)

genomeIntervals documentation built on Nov. 8, 2020, 4:56 p.m.