Description Usage Arguments Value Examples
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).
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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 |
data frame with TAD positions containing start, end columns
1 2 3 4 5 6 7 8 | # 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)
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