intervalsDist: intervalsDist

In bioinfo-pf-curie/HiTC: High Throughput Chromosome Conformation Capture analysis

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)

bioinfo-pf-curie/HiTC documentation built on May 17, 2019, 6:39 p.m.