map2tads: Determines TAD boundaries using Insulation Score.

Description Usage Arguments Value Examples

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

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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

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# 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/CopulaHiC documentation built on Dec. 31, 2019, 9:19 a.m.