get.combination.count

vector of bait IDs in form chrN:start-end

baits

vector of fragment IDs in form chrN:start-end

fragments

logical indicating whether cis-interactions only should be considered

cis.only

Calculate the number of possible combinations between baits and fragments, 
	excluding self-ligations and only counting bait-to-bait interactions once (e.g. a-b, not b-a)

Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.

get.combination.count: get.combination.count

Description

Usage

Arguments

Value