intervalsDist {HiTC}R Documentation

intervalsDist

Description

Compute the distance of intrachromosomal contacts of a 'C' experiment

Usage

intervalsDist(x, use.zero=TRUE)

Arguments

x

object that inherits from class HTCexp

use.zero

if FALSE, the distance for non interacting regions (zero counts) are not reported

Details

If A and B are the two sets of intervals and s and e, the start and end of an interval, the distance is calculated as :

\min(|A_e - B_s|, |A_s - B_e|)

Only intrachromsomal contact maps can be use for this operation.

Value

A matrix of distances between genomic intervals

Author(s)

N. Servant

See Also

HTCexp-class

Examples

data(Nora_5C)

## Calculate distances between primers/intervals
d<-intervalsDist(E14$chrXchrX)

[Package HiTC version 1.36.0 Index]