incl/overlapScores.R

In HenrikBengtsson/TopDom: An Efficient and Deterministic Method for Identifying Topological Domains in Genomes

library(tibble)
path <- system.file("exdata", package = "TopDom", mustWork = TRUE)

## Original count data (on a subset of the bins to speed up example)
chr <- "chr19"
pathname <- file.path(path, sprintf("nij.%s.gz", chr))
data <- readHiC(pathname, chr = chr, binSize = 40e3, bins = 1:500)
print(data)

## Find topological domains using TopDom method for two window sizes
tds_5 <- TopDom(data, window.size = 5L)
tds_6 <- TopDom(data, window.size = 6L)

## Overlap scores (in both directions)
overlap_56 <- overlapScores(tds_6, reference = tds_5)
print(overlap_56)
print(as_tibble(overlap_56))

overlap_65 <- overlapScores(tds_5, reference = tds_6)
print(overlap_65)
print(as_tibble(overlap_65))