Quickly computes a cis-trans ratio of interactions.
cisTransRatio(x)A HiCExperiment object over the full genome
a tibble, listing for each chr. the % of cis/trans interactions
library(HiContacts)
full_contacts_yeast <- contacts_yeast(full = TRUE)
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
cisTransRatio(full_contacts_yeast)
#> # A tibble: 16 × 6
#> # Groups: chr [16]
#> chr cis trans n_total cis_pct trans_pct
#> <fct> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 I 186326 96738 283064 0.658 0.342
#> 2 II 942728 273966 1216694 0.775 0.225
#> 3 III 303980 127087 431067 0.705 0.295
#> 4 IV 1858062 418218 2276280 0.816 0.184
#> 5 V 607090 220873 827963 0.733 0.267
#> 6 VI 280282 127771 408053 0.687 0.313
#> 7 VII 1228532 335909 1564441 0.785 0.215
#> 8 VIII 574086 205122 779208 0.737 0.263
#> 9 IX 474182 179280 653462 0.726 0.274
#> 10 X 834656 259240 1093896 0.763 0.237
#> 11 XI 775240 245899 1021139 0.759 0.241
#> 12 XII 1182742 278065 1460807 0.810 0.190
#> 13 XIII 1084810 296351 1381161 0.785 0.215
#> 14 XIV 852516 256639 1109155 0.769 0.231
#> 15 XV 1274070 351132 1625202 0.784 0.216
#> 16 XVI 1070700 313520 1384220 0.774 0.226