intra_inter_TAD: Intra and inter TAD contacts

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

Intra and inter TAD contacts

Description

Calculate the coverage over TADs and between a TAD and its neighbours.

Usage

intra_inter_TAD(explist, tad_bed, max_neighbour = 5)

Arguments

explist	Either a single GENOVA contacts object or a list of GENOVA contacts objects.
tad_bed	A BED-formatted data.frame with three columns containing the chromosome name, start- and end-positions of non-overlapping TADs.
max_neighbour	An integer of length 1 indicating how many neighbouring TADs to take into account.

Details

The TADs are expected to be consecutive: the 3' border of a TAD is the same position as the 5' border of the subsequent TAD.

Although the explist argument is allowed to be a different resolution than whence the TAD calls came, it is discouraged to use higher basepair resolution for the explist argument compared to the TAD calls for accuracy reasons.

Value

An IIT_discovery object containing the following slots:

results

A data.table with two columns of left and right TAD identifiers and scores for the experiments in explist.

tads

The tad_bed argument supplemented with TAD identifiers used in the results slot.

Resolution recommendation

The same resolution as whence the TADs were called.

See Also

For calling TADs with insulation scores, see insulation_score() and call_TAD_insulation. For calling TADs with HiCseg, see HiCseg.callTAD.

Examples

## Not run: 
# Getting TAD calls
insula <- insulation_score(WT_20kb)
tads <- call_TAD_insulation(insula)[[1]]

# Calculating the inter-intra TAD contacts
iit <- intra_inter_TAD(list(WT_20kb, KO_20kb), tads)

## End(Not run)

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