map2tads: Determines TAD boundaries using Insulation Score.

In rz6/DIADEM: Hi-C differential analysis via dependency modelling of chromatin interactions with generalized linear models

Description

For details on Insulation Score approach of TAD boundaries detection see Crane et al. 2015 "Condensin-driven remodelling of X chromosome topology during dosage compensation" methods section, paragraph TAD calling (insulation square analysis).

Usage

map2tads(
  dense.mtx,
  resolution = 40000,
  window.bp = 500 * 1000,
  delta.bp = 100 * 1000,
  without_unmappable = TRUE
)

Arguments

dense.mtx	numeric matrix in dense format representing Hi-C contact map
resolution	numeric resolution of Hi-C contact map in base pairs
window.bp	numeric size of sliding window in base pairs
delta.bp	numeic size of delta window in base pairs

Value

data frame with TAD positions containing start, end columns

Examples

# get Hi-C contact map
sparse.mtx <- DIADEM::sample_hic_maps[["MSC-HindIII-1_40kb-raw"]][["18"]]
dense.mtx <- sparse2dense(sparse.mtx[c("i","j","val")], N = 1952)
# get tads
tads <- map2tads(dense.mtx)
# plot results
plot_contact_map(dense.mtx)
plot_regions(tads)

rz6/DIADEM documentation built on Dec. 31, 2019, 3:51 a.m.