direct_index: Directionality index

In robinweide/GENOVA: GENOVA: expore the Hi-C

Directionality index

Description

The directionality index quantifies the degree of bias between upstream and downstream interactions given a bin on the diagonal. Such biases become apparent near the periphery of TADs: the upstream portion of a TAD interacts more with the downstream bins and inversely, the downstream portion of a TAD interacts more with the upstream bins.

Usage

direct_index(explist, range = 100)

Arguments

explist	Either a single GENOVA contacts object or list of GENOVA contacts.
range	An integer of length 1 indicating how many bins from the diagonal should be considered.

Details

The directionality index is computed as described in Dixon et al. (2012):

DI = (\frac{B - A}{|B - A|})

Wherein A and B are the sum of the contacts up- and downstream of a bin on the diagonal respectively, and E = (A + B)/2.

The first part signs the second part of the equation by the direction of the effect. The \chi^2 test statistics can be recognised in the second part of the equation with a null-hypothesis that the upstream and downstream signal is equal.

The authors originally used a 40kb matrix with a 2Mb range, equivalent to range = 50.

Value

A DI_discovery object containing a directionality index for every informative bin.

Examples

## Not run: 
# As original authors
di <- direct_index(list(WT_40kb, KO_40kb), range = 50)

# Plotting the DI
visualise(di)

## End(Not run)

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.