interval_overlap-methods: Assess overlap from one set of genomic intervals to another

Description Usage Arguments Details Value Examples

Description

Given two objects, a 'from' and a 'to', assess which intervals in 'to' overlap which of 'from'.

Usage

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## S4 method for signature 'Genome_intervals,Genome_intervals'
interval_overlap(
                 from, to,
                 check_valid = TRUE
                 )
## S4 method for signature 
## 'Genome_intervals_stranded,Genome_intervals_stranded'
interval_overlap(
                 from, to,
                 check_valid = TRUE
                 )

Arguments

from

A Genome_intervals or Genome_intervals_stranded object.

to

A Genome_intervals or Genome_intervals_stranded object.

check\_valid

Should validObject be called before passing to compiled code?

Details

A wrapper calling intervals:interval_overlap by seq_name and by strand (if both to and from are "Genome_intervals_stranded" objects).

Value

A list, with one element for each row of from. The elements are vectors of indices, indicating which to rows overlap each from. A list element of length 0 indicates a from with no overlapping to intervals.

Examples

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data(gen_ints)	 
# i as entered
i

# i in close_intervals notation
close_intervals(i)
 
# j in close_intervals notation
close_intervals(j)
 
# list of intervals of j overlapping intervals of i
interval_overlap(i,j)
	 

genomeIntervals documentation built on Nov. 1, 2018, 3:48 a.m.