vignettes/TopDomStudy-3.Overview_of_Ramani_Data.md
In HenrikBengtsson/TopDomStudy: TopDom Study by Segal et al.
%\VignetteIndexEntry{TopDomStudy: Overview of the Ramani Data}
%\VignetteAuthor{Henrik Bengtsson}
%\VignetteEngine{TopDomStudy::self}
%\VignetteEncoding{UTF-8}
%\VignetteKeyword{R}
%\VignetteKeyword{package}
%\VignetteKeyword{vignette}
Organism: human
Sample: GSM2254215_ML1,human,unique.rds
# A tibble: 8,882,447 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 648845 648891 1 16381046 16381090 HAP1 27
2 1 706635 706674 1 715083 715157 HAP1 34
3 1 706635 706674 1 1060448 1060506 HAP1 35
4 1 706635 706674 1 1145206 1145262 HAP1 36
5 1 712858 712888 1 223872404 223872539 HeLa 37
6 1 715255 715294 1 930962 931037 HAP1 40
7 1 718586 718645 1 718649 718768 HeLa 44
8 1 718586 718645 1 926191 926430 HeLa 45
9 1 718649 718768 1 7054834 7054981 HeLa 47
10 1 718649 718768 1 188962955 188962987 HeLa 48
# ... with 8,882,437 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 248577926 818998 329.47334
2 2 243173514 698740 287.34215
3 3 197856630 664917 336.06000
4 4 191021317 452415 236.84006
5 5 180716869 681489 377.10315
6 6 170774596 474957 278.11924
7 7 159085421 482986 303.60167
8 8 146148464 486827 333.10442
9 9 141105119 365828 259.25920
10 10 135440110 399152 294.70738
11 11 134793608 460875 341.91161
12 12 133773941 447407 334.45004
13 13 96088673 252606 262.88843
14 14 88286222 277416 314.22344
15 15 82473935 320116 388.14202
16 16 90208853 227213 251.87439
17 17 81159168 229978 283.36663
18 18 78002091 214890 275.49261
19 19 59008537 150901 255.72740
20 20 62905359 199250 316.74567
21 21 38703277 92826 239.84016
22 22 34996300 75846 216.72577
23 M 15549 112 720.30356
24 X 153569965 406694 264.82652
25 Y 46580 8 17.17475
Cell types:
HAP1 HeLa
2998051 5041548
Sample: GSM2254216_ML2,human,unique.rds
# A tibble: 7,244,237 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 91157 91258 1 227935823 227935868 HeLa 8
2 1 126153 126339 1 31206229 31206347 HeLa 24
3 1 648845 648891 1 1809163 1809226 HeLa 31
4 1 651131 651255 1 109986897 109987136 HeLa 32
5 1 706635 706674 1 51529139 51529378 HeLa 34
6 1 712981 713019 1 5868412 5868478 HeLa 36
7 1 715083 715157 1 862142 862192 HAP1 37
8 1 715255 715294 1 945712 945803 HeLa 2
9 1 716222 716252 1 1104425 1104469 <NA> 6
10 1 718586 718645 1 720638 720687 HAP1 42
# ... with 7,244,227 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 249133387 666826 267.65822
2 2 243166497 573636 235.90256
3 3 197861763 538647 272.23400
4 4 191021317 368004 192.65075
5 5 180769703 547508 302.87597
6 6 170843820 380697 222.83335
7 7 159094994 391518 246.09071
8 8 146183718 394485 269.85563
9 9 141129459 296977 210.42878
10 10 135439004 332180 245.26170
11 11 134810407 379406 281.43673
12 12 133756706 364031 272.15906
13 13 96044293 198944 207.13776
14 14 88286019 226269 256.29086
15 15 82459934 262863 318.77663
16 16 90229431 190825 211.48864
17 17 81159294 187819 231.42020
18 18 78004121 174343 223.50486
19 19 58870280 131034 222.58090
20 20 62904872 165082 262.43118
21 21 38683087 73960 191.19467
22 22 34804817 65295 187.60334
23 M 16146 48 297.28725
24 X 152573171 333834 218.80256
25 Y 53014 6 11.31777
Cell types:
HAP1 HeLa
2698488 3831724
Sample: GSM2254217_ML3,human,unique.rds
# A tibble: 3,117,958 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 124901 124934 1 43831291 43831325 GM12878 2
2 1 603264 603503 1 30741246 30741322 K562 9
3 1 706635 706674 1 926533 926650 K562 12
4 1 706635 706674 1 39341389 39341430 K562 13
5 1 715035 715157 1 155479070 155479128 GM12878 14
6 1 716222 716252 1 1314922 1314965 K562 15
7 1 718586 718645 1 31580001 31580035 K562 16
8 1 718587 718645 1 1334579 1334628 K562 18
9 1 718649 718768 1 204451866 204451951 K562 19
10 1 718863 718900 1 981127 981224 K562 20
# ... with 3,117,948 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 249101870 296990 119.224316
2 2 243167132 272456 112.044748
3 3 197834444 219272 110.836109
4 4 191003635 195819 102.521086
5 5 180701648 204558 113.202067
6 6 170847389 203225 118.951189
7 7 159086004 194135 122.031477
8 8 146148464 161506 110.508175
9 9 141033507 106822 75.742284
10 10 135390830 143835 106.236885
11 11 134766753 151221 112.209426
12 12 133755823 143842 107.540739
13 13 96053232 88434 92.067698
14 14 88285506 81461 92.269959
15 15 82498878 85742 103.931110
16 16 90181661 83991 93.135344
17 17 81149871 78370 96.574399
18 18 78003870 78345 100.437324
19 19 58866600 61557 104.570334
20 20 62903563 64816 103.040268
21 21 38687712 37771 97.630483
22 22 34888702 38750 111.067474
23 M 16146 59 365.415583
24 X 152225528 124977 82.099896
25 Y 51251 4 7.804726
Cell types:
GM12878 K562
1408745 1541638
Sample: GSM2254218_PL1,human,unique.rds
# A tibble: 8,855,074 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 61943 62182 1 121281494 121281534 HeLa 7
2 1 68255 68327 1 17465738 17465894 HeLa 8
3 1 87117 87212 1 199945185 199945277 HeLa 14
4 1 124901 124934 1 113159319 113159505 HAP1 16
5 1 636630 636760 1 996345 996417 HeLa 28
6 1 636630 636760 1 22064488 22064613 HeLa 29
7 1 648845 648891 1 874123 874174 HAP1 31
8 1 673118 673335 1 787985 788054 HeLa 35
9 1 713195 713271 1 45604332 45604395 HeLa 38
10 1 713195 713271 1 113942769 113943008 HeLa 39
# ... with 8,855,064 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 249166541 799335 320.80350628
2 2 243164057 710935 292.36845641
3 3 197855369 702103 354.85668322
4 4 191003984 493838 258.54853373
5 5 180704848 742034 410.63314472
6 6 170759858 496582 290.80722239
7 7 159084284 493923 310.47881512
8 8 146183304 505757 345.97453072
9 9 141085170 348075 246.71267717
10 10 135447449 380771 281.12083528
11 11 134757600 444944 330.18100649
12 12 133778432 454589 339.80739137
13 13 96047049 272110 283.30906866
14 14 88289313 280789 318.03282918
15 15 82453036 298571 362.11037760
16 16 90205035 194762 215.91034248
17 17 81108641 182801 225.37795942
18 18 78002091 223295 286.26796684
19 19 59007662 94453 160.06904324
20 20 62905447 166108 264.05980391
21 21 38687383 94335 243.83918654
22 22 35149308 49507 140.84772309
23 M 15549 15 96.46922632
24 X 152228929 425436 279.47119039
25 Y 55309122 6 0.01084812
Cell types:
HAP1 HeLa MEF Patski
2205906 6649082 1 2
Sample: GSM2254219_PL2,human,unique.rds
# A tibble: 13,912,930 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 636631 636760 1 1178972 1179158 HAP1 58
2 1 648845 648891 1 706635 706674 HeLa 59
3 1 648845 648891 1 738044 738186 HeLa 7
4 1 648845 648891 1 858596 858642 HeLa 60
5 1 648845 648891 1 3462656 3462732 HAP1 61
6 1 648845 648891 1 7571262 7571396 HeLa 62
7 1 651131 651255 1 787985 788054 HeLa 67
8 1 651131 651255 1 46975161 46975272 HeLa 68
9 1 651131 651255 1 113629995 113630033 HeLa 69
10 1 672179 672220 1 1687827 1688035 HeLa 70
# ... with 13,912,920 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 248598234 1303235 524.23341028
2 2 243174534 1081787 444.86031584
3 3 197861763 1052911 532.14475806
4 4 191014876 680513 356.26178141
5 5 180716869 1109566 613.98031415
6 6 170718280 732517 429.07941669
7 7 159087445 760501 478.03960897
8 8 146274620 773008 528.46351609
9 9 141129459 569198 403.31622046
10 10 135440109 616809 455.41088571
11 11 134784419 742902 551.17795181
12 12 133756705 700715 523.87280324
13 13 96060333 379412 394.97260539
14 14 88286192 435617 493.41464405
15 15 82498740 495383 600.47341329
16 16 90225070 358919 397.80406931
17 17 81159168 352999 434.94654849
18 18 78004121 334153 428.37864938
19 19 59017259 229126 388.23558376
20 20 62905359 314623 500.15293610
21 21 38685809 146084 377.61650532
22 22 35030625 110792 316.27183357
23 M 15970 47 294.30181590
24 X 152228929 632103 415.23185123
25 Y 55317404 10 0.01807749
Cell types:
HAP1 HeLa MEF Patski
3194182 10713017 1 3
Sample: GSM2438426_ML4,human,unique.rds
# A tibble: 27,021,519 x 8
# Groups: chr_a [23]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 61887 62082 1 101667 101735 Nocadazole 20
2 1 61887 62082 1 247984 248051 Nocadazole 20
3 1 101667 101735 1 1885181 1885349 Nocadazole 54
4 1 124901 124934 1 96664199 96664266 Nocadazole 91
5 1 235158 235188 1 52253263 52253497 Asynchronous 120
6 1 562004 562081 1 20898624 20898764 Nocadazole 153
7 1 636630 636760 1 6425671 6425911 Nocadazole 157
8 1 636630 636760 1 27252279 27252419 Nocadazole 74
9 1 648845 648891 1 1517212 1517252 Nocadazole 159
10 1 648845 648891 1 4754301 4754455 Nocadazole 160
# ... with 27,021,509 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 249172978 2664364 1069.2829
2 2 243174534 1982115 815.0997
3 3 197861763 2015873 1018.8290
4 4 191011988 1128153 590.6190
5 5 180716869 2251626 1245.9412
6 6 170798397 1338128 783.4547
7 7 159094994 1457537 916.1426
8 8 146274593 1517530 1037.4529
9 9 141105245 1154848 818.4302
10 10 135448202 1197094 883.8021
11 11 134783335 1464853 1086.8206
12 12 133779100 1384026 1034.5607
13 13 96080185 680431 708.1908
14 14 88288101 858766 972.6860
15 15 82470913 980615 1189.0435
16 16 90208752 738362 818.5037
17 17 81171113 744759 917.5173
18 18 78004121 623718 799.5962
19 19 58879204 502206 852.9429
20 20 62905359 657318 1044.9316
21 21 38697772 291427 753.0847
22 22 35182925 214882 610.7565
23 X 154118408 1172888 761.0304
Cell types:
Asynchronous Nocadazole
9677605 16710710
Organism: mouse
Sample: GSM2254215_ML1,mouse,unique.rds
# A tibble: 4,002,891 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000983 3001047 1 4965798 4965885 MEF 1
2 1 3001122 3001293 1 3074714 3074770 Patski 2
3 1 3003353 3003418 1 4320235 4320402 MEF 3
4 1 3003486 3003575 1 3006173 3006412 MEF 4
5 1 3003486 3003575 1 3008062 3008094 Patski 5
6 1 3003604 3003815 1 3007753 3007894 Patski 6
7 1 3003604 3003815 1 4337484 4337520 Patski 7
8 1 3003944 3004012 1 4022994 4023131 Patski 8
9 1 3004055 3004111 1 9903838 9903888 MEF 9
10 1 3005547 3005760 1 4366159 4366227 Patski 10
# ... with 4,002,881 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192370575 298510 155.17445950
2 2 178961532 298348 166.71068730
3 3 156938025 398025 253.61922326
4 4 153294221 140135 91.41570966
5 5 148727398 303031 203.74927826
6 6 146528721 233740 159.51821486
7 7 142332981 193032 135.62000785
8 8 126224923 203117 160.91671531
9 9 121455460 198246 163.22526793
10 10 127491527 199774 156.69590341
11 11 118870753 193454 162.74314339
12 12 117016944 132611 113.32632307
13 13 117318086 166621 142.02499008
14 14 121795777 151282 124.20956106
15 15 100888736 172940 171.41655933
16 16 94873635 147998 155.99486622
17 17 91886447 150221 163.48548116
18 18 87598479 135896 155.13511370
19 19 58252297 92433 158.67700462
20 M 14403 36 249.94792752
21 X 166912961 193417 115.87895802
22 Y 37584000 24 0.06385696
Cell types:
MEF Patski
202759 3450173
Sample: GSM2254216_ML2,mouse,unique.rds
# A tibble: 2,929,110 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3003604 3003815 1 70492182 70492319 <NA> 2
2 1 3003812 3004012 1 3717382 3717465 Patski 3
3 1 3004324 3004563 1 21621468 21621554 Patski 4
4 1 3005547 3005760 1 67040987 67041061 Patski 5
5 1 3006173 3006309 1 3009141 3009232 Patski 6
6 1 3007305 3007389 1 6836946 6836980 Patski 7
7 1 3007753 3007894 1 15516931 15517005 MEF 10
8 1 3008375 3008408 1 3011419 3011451 MEF 11
9 1 3008412 3008485 1 3451673 3451726 Patski 12
10 1 3009056 3009103 1 3589463 3589516 Patski 13
# ... with 2,929,100 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192367954 217400 113.01258629
2 2 178961532 216137 120.77288207
3 3 156936036 275368 175.46511752
4 4 153201184 109521 71.48835090
5 5 148720774 213645 143.65511573
6 6 146530342 172419 117.66777969
7 7 142332839 148740 104.50153390
8 8 126265160 151005 119.59356009
9 9 121447043 147119 121.13839610
10 10 127493471 146113 114.60430001
11 11 118871165 145708 122.57640446
12 12 117026794 99054 84.64215468
13 13 117318982 121788 103.80928808
14 14 121795734 110786 90.96049292
15 15 100888668 127878 126.75159910
16 16 95021314 108288 113.96180019
17 17 91886612 112149 122.05151279
18 18 87599334 98157 112.05222177
19 19 58248179 68955 118.38138322
20 M 14403 9 62.48698188
21 X 166929063 138830 83.16706360
22 Y 86183943 41 0.04757267
Cell types:
MEF Patski
350996 2314028
Sample: GSM2254217_ML3,mouse,unique.rds
# A tibble: 741,760 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000984 3001047 1 23351683 23351757 MEF 1
2 1 3006173 3006309 1 3006531 3006563 MEF 2
3 1 3007393 3007454 1 4326789 4326851 Patski 3
4 1 3008354 3008408 1 4710734 4710973 Patski 4
5 1 3012619 3012668 1 5178289 5178348 <NA> 5
6 1 3013262 3013309 1 36929665 36929724 Patski 3
7 1 3014512 3014555 1 18533138 18533187 MEF 6
8 1 3028842 3028900 1 22733715 22733776 MEF 7
9 1 3032078 3032164 1 3048394 3048459 MEF 8
10 1 3035765 3035841 1 31976505 31976552 MEF 10
# ... with 741,750 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192369584 56693 29.4708752
2 2 178960181 55646 31.0940678
3 3 156937414 55988 35.6753680
4 4 153266009 34625 22.5914410
5 5 148729365 47085 31.6581732
6 6 146525804 42927 29.2965463
7 7 142323304 38728 27.2112851
8 8 126254719 38079 30.1604568
9 9 121414022 39131 32.2293911
10 10 127493829 38343 30.0743968
11 11 118869954 38668 32.5296668
12 12 116996617 30215 25.8255331
13 13 117284693 32219 27.4707630
14 14 120777208 29810 24.6818092
15 15 100886702 31822 31.5423137
16 16 94872481 28118 29.6376775
17 17 91880893 26514 28.8569246
18 18 87594240 26649 30.4232333
19 19 58218505 19262 33.0857002
20 M 14079 19 134.9527665
21 X 166772990 31175 18.6930749
22 Y 43187668 44 0.1018809
Cell types:
MEF Patski
399235 239268
Sample: GSM2254218_PL1,mouse,unique.rds
# A tibble: 9,055,515 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000748 3000812 1 17336484 17336681 Patski 1
2 1 3000816 3000985 1 5889797 5889855 Patski 2
3 1 3000816 3000985 1 6666639 6666751 Patski 3
4 1 3000816 3000985 1 108504418 108504593 Patski 1
5 1 3000816 3000985 1 166212738 166212800 Patski 4
6 1 3000983 3001118 1 3008062 3008094 Patski 5
7 1 3000983 3001047 1 47091788 47091885 Patski 6
8 1 3000987 3001047 1 3067986 3068071 MEF 7
9 1 3001798 3002017 1 4341744 4341842 Patski 8
10 1 3003213 3003265 1 3657464 3657537 MEF 9
# ... with 9,055,505 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192370810 715843 372.1162270
2 2 178962007 663246 370.6071535
3 3 156938493 917870 584.8597004
4 4 153294811 301060 196.3928185
5 5 148732122 650775 437.5483865
6 6 146535828 537661 366.9143631
7 7 142338970 382479 268.7099675
8 8 126287205 443059 350.8344333
9 9 121449203 424215 349.2941819
10 10 127493829 485796 381.0349127
11 11 118875997 399061 335.6951866
12 12 117026963 319604 273.1028746
13 13 117320155 365252 311.3292852
14 14 121795777 344762 283.0656436
15 15 100890015 379861 376.5100045
16 16 95009733 349307 367.6539118
17 17 91885487 322803 351.3101041
18 18 87600284 315553 360.2191518
19 19 58252249 216572 371.7830706
20 M 14403 133 923.4187322
21 X 166934731 520441 311.7631645
22 Y 90041618 162 0.1799168
Cell types:
HAP1 HeLa MEF Patski
9 6 1146613 7908776
Sample: GSM2254219_PL2,mouse,unique.rds
# A tibble: 16,115,940 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000194 3000290 1 3380053 3380083 Patski 1
2 1 3000194 3000356 1 28278273 28278326 Patski 2
3 1 3000748 3000812 1 3036826 3036882 Patski 3
4 1 3000748 3000812 1 4321086 4321202 Patski 4
5 1 3000748 3000812 1 4339680 4339919 Patski 5
6 1 3000748 3000812 1 21180408 21180507 Patski 6
7 1 3000816 3000985 1 4223507 4223574 Patski 7
8 1 3000816 3000985 1 15453757 15453795 MEF 8
9 1 3000983 3001047 1 6537085 6537185 MEF 10
10 1 3003212 3003265 1 3034166 3034210 MEF 11
# ... with 16,115,930 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192371364 1235406 642.1984927
2 2 178962532 1196485 668.5673178
3 3 156938737 1500226 955.9309758
4 4 153306207 560631 365.6936082
5 5 148732157 1204207 809.6480440
6 6 146536084 956644 652.8385186
7 7 142338970 769031 540.2814141
8 8 126291290 820960 650.0527471
9 9 121494312 787839 648.4575179
10 10 127493829 830169 651.1444566
11 11 118876754 778814 655.1440663
12 12 117027004 558245 477.0223802
13 13 117319628 644301 549.1843189
14 14 121796062 598152 491.1094745
15 15 100888736 698341 692.1892648
16 16 94948659 604074 636.2111970
17 17 91886251 613980 668.1957239
18 18 87600284 544631 621.7228702
19 19 58248233 392717 674.2127268
20 M 14492 202 1393.8724814
21 X 167622474 820714 489.6205028
22 Y 90002613 171 0.1899945
Cell types:
HAP1 HeLa MEF Patski
82 44 1971223 14142703
Sample: GSM2438426_ML4,mouse,unique.rds
# A tibble: 3,156,550 x 8
# Groups: chr_a [20]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000983 3001118 1 46187073 46187119 Patski 1
2 1 3003486 3003575 1 3007753 3007893 Patski 2
3 1 3003486 3003600 1 3010457 3010499 Patski 3
4 1 3003486 3003575 1 6887703 6887841 <NA> 4
5 1 3003812 3004051 1 3266448 3266508 Patski 6
6 1 3007393 3007461 1 3012057 3012248 Patski 8
7 1 3008104 3008339 1 3008412 3008479 Patski 9
8 1 3008412 3008485 1 3009117 3009232 Patski 10
9 1 3008691 3008930 1 39786341 39786393 Patski 11
10 1 3009056 3009103 1 5662792 5662882 Patski 12
# ... with 3,156,540 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192370540 232374 120.79500
2 2 178961681 234286 130.91406
3 3 156938025 296009 188.61522
4 4 153271232 93474 60.98600
5 5 148727392 218531 146.93393
6 6 146529099 186966 127.59650
7 7 142330101 151370 106.35136
8 8 126221514 165131 130.82635
9 9 121445094 163369 134.52087
10 10 127492417 155766 122.17668
11 11 118874181 167034 140.51327
12 12 117017815 125093 106.90082
13 13 117317002 131356 111.96672
14 14 121779385 121738 99.96602
15 15 100879823 135975 134.78909
16 16 94866594 116172 122.45828
17 17 91886144 115494 125.69251
18 18 87599626 107904 123.17861
19 19 58247109 96674 165.97219
20 X 167488146 141834 84.68301
Cell types:
Patski
2729322
HenrikBengtsson/TopDomStudy documentation built on May 14, 2021, 1:49 p.m.
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%\VignetteIndexEntry{TopDomStudy: Overview of the Ramani Data} %\VignetteAuthor{Henrik Bengtsson} %\VignetteEngine{TopDomStudy::self} %\VignetteEncoding{UTF-8} %\VignetteKeyword{R} %\VignetteKeyword{package} %\VignetteKeyword{vignette}
Organism: human
Sample: GSM2254215_ML1,human,unique.rds
# A tibble: 8,882,447 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 648845 648891 1 16381046 16381090 HAP1 27
2 1 706635 706674 1 715083 715157 HAP1 34
3 1 706635 706674 1 1060448 1060506 HAP1 35
4 1 706635 706674 1 1145206 1145262 HAP1 36
5 1 712858 712888 1 223872404 223872539 HeLa 37
6 1 715255 715294 1 930962 931037 HAP1 40
7 1 718586 718645 1 718649 718768 HeLa 44
8 1 718586 718645 1 926191 926430 HeLa 45
9 1 718649 718768 1 7054834 7054981 HeLa 47
10 1 718649 718768 1 188962955 188962987 HeLa 48
# ... with 8,882,437 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 248577926 818998 329.47334
2 2 243173514 698740 287.34215
3 3 197856630 664917 336.06000
4 4 191021317 452415 236.84006
5 5 180716869 681489 377.10315
6 6 170774596 474957 278.11924
7 7 159085421 482986 303.60167
8 8 146148464 486827 333.10442
9 9 141105119 365828 259.25920
10 10 135440110 399152 294.70738
11 11 134793608 460875 341.91161
12 12 133773941 447407 334.45004
13 13 96088673 252606 262.88843
14 14 88286222 277416 314.22344
15 15 82473935 320116 388.14202
16 16 90208853 227213 251.87439
17 17 81159168 229978 283.36663
18 18 78002091 214890 275.49261
19 19 59008537 150901 255.72740
20 20 62905359 199250 316.74567
21 21 38703277 92826 239.84016
22 22 34996300 75846 216.72577
23 M 15549 112 720.30356
24 X 153569965 406694 264.82652
25 Y 46580 8 17.17475
Cell types:
HAP1 HeLa
2998051 5041548
Sample: GSM2254216_ML2,human,unique.rds
# A tibble: 7,244,237 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 91157 91258 1 227935823 227935868 HeLa 8
2 1 126153 126339 1 31206229 31206347 HeLa 24
3 1 648845 648891 1 1809163 1809226 HeLa 31
4 1 651131 651255 1 109986897 109987136 HeLa 32
5 1 706635 706674 1 51529139 51529378 HeLa 34
6 1 712981 713019 1 5868412 5868478 HeLa 36
7 1 715083 715157 1 862142 862192 HAP1 37
8 1 715255 715294 1 945712 945803 HeLa 2
9 1 716222 716252 1 1104425 1104469 <NA> 6
10 1 718586 718645 1 720638 720687 HAP1 42
# ... with 7,244,227 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 249133387 666826 267.65822
2 2 243166497 573636 235.90256
3 3 197861763 538647 272.23400
4 4 191021317 368004 192.65075
5 5 180769703 547508 302.87597
6 6 170843820 380697 222.83335
7 7 159094994 391518 246.09071
8 8 146183718 394485 269.85563
9 9 141129459 296977 210.42878
10 10 135439004 332180 245.26170
11 11 134810407 379406 281.43673
12 12 133756706 364031 272.15906
13 13 96044293 198944 207.13776
14 14 88286019 226269 256.29086
15 15 82459934 262863 318.77663
16 16 90229431 190825 211.48864
17 17 81159294 187819 231.42020
18 18 78004121 174343 223.50486
19 19 58870280 131034 222.58090
20 20 62904872 165082 262.43118
21 21 38683087 73960 191.19467
22 22 34804817 65295 187.60334
23 M 16146 48 297.28725
24 X 152573171 333834 218.80256
25 Y 53014 6 11.31777
Cell types:
HAP1 HeLa
2698488 3831724
Sample: GSM2254217_ML3,human,unique.rds
# A tibble: 3,117,958 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 124901 124934 1 43831291 43831325 GM12878 2
2 1 603264 603503 1 30741246 30741322 K562 9
3 1 706635 706674 1 926533 926650 K562 12
4 1 706635 706674 1 39341389 39341430 K562 13
5 1 715035 715157 1 155479070 155479128 GM12878 14
6 1 716222 716252 1 1314922 1314965 K562 15
7 1 718586 718645 1 31580001 31580035 K562 16
8 1 718587 718645 1 1334579 1334628 K562 18
9 1 718649 718768 1 204451866 204451951 K562 19
10 1 718863 718900 1 981127 981224 K562 20
# ... with 3,117,948 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 249101870 296990 119.224316
2 2 243167132 272456 112.044748
3 3 197834444 219272 110.836109
4 4 191003635 195819 102.521086
5 5 180701648 204558 113.202067
6 6 170847389 203225 118.951189
7 7 159086004 194135 122.031477
8 8 146148464 161506 110.508175
9 9 141033507 106822 75.742284
10 10 135390830 143835 106.236885
11 11 134766753 151221 112.209426
12 12 133755823 143842 107.540739
13 13 96053232 88434 92.067698
14 14 88285506 81461 92.269959
15 15 82498878 85742 103.931110
16 16 90181661 83991 93.135344
17 17 81149871 78370 96.574399
18 18 78003870 78345 100.437324
19 19 58866600 61557 104.570334
20 20 62903563 64816 103.040268
21 21 38687712 37771 97.630483
22 22 34888702 38750 111.067474
23 M 16146 59 365.415583
24 X 152225528 124977 82.099896
25 Y 51251 4 7.804726
Cell types:
GM12878 K562
1408745 1541638
Sample: GSM2254218_PL1,human,unique.rds
# A tibble: 8,855,074 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 61943 62182 1 121281494 121281534 HeLa 7
2 1 68255 68327 1 17465738 17465894 HeLa 8
3 1 87117 87212 1 199945185 199945277 HeLa 14
4 1 124901 124934 1 113159319 113159505 HAP1 16
5 1 636630 636760 1 996345 996417 HeLa 28
6 1 636630 636760 1 22064488 22064613 HeLa 29
7 1 648845 648891 1 874123 874174 HAP1 31
8 1 673118 673335 1 787985 788054 HeLa 35
9 1 713195 713271 1 45604332 45604395 HeLa 38
10 1 713195 713271 1 113942769 113943008 HeLa 39
# ... with 8,855,064 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 249166541 799335 320.80350628
2 2 243164057 710935 292.36845641
3 3 197855369 702103 354.85668322
4 4 191003984 493838 258.54853373
5 5 180704848 742034 410.63314472
6 6 170759858 496582 290.80722239
7 7 159084284 493923 310.47881512
8 8 146183304 505757 345.97453072
9 9 141085170 348075 246.71267717
10 10 135447449 380771 281.12083528
11 11 134757600 444944 330.18100649
12 12 133778432 454589 339.80739137
13 13 96047049 272110 283.30906866
14 14 88289313 280789 318.03282918
15 15 82453036 298571 362.11037760
16 16 90205035 194762 215.91034248
17 17 81108641 182801 225.37795942
18 18 78002091 223295 286.26796684
19 19 59007662 94453 160.06904324
20 20 62905447 166108 264.05980391
21 21 38687383 94335 243.83918654
22 22 35149308 49507 140.84772309
23 M 15549 15 96.46922632
24 X 152228929 425436 279.47119039
25 Y 55309122 6 0.01084812
Cell types:
HAP1 HeLa MEF Patski
2205906 6649082 1 2
Sample: GSM2254219_PL2,human,unique.rds
# A tibble: 13,912,930 x 8
# Groups: chr_a [25]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 636631 636760 1 1178972 1179158 HAP1 58
2 1 648845 648891 1 706635 706674 HeLa 59
3 1 648845 648891 1 738044 738186 HeLa 7
4 1 648845 648891 1 858596 858642 HeLa 60
5 1 648845 648891 1 3462656 3462732 HAP1 61
6 1 648845 648891 1 7571262 7571396 HeLa 62
7 1 651131 651255 1 787985 788054 HeLa 67
8 1 651131 651255 1 46975161 46975272 HeLa 68
9 1 651131 651255 1 113629995 113630033 HeLa 69
10 1 672179 672220 1 1687827 1688035 HeLa 70
# ... with 13,912,920 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 248598234 1303235 524.23341028
2 2 243174534 1081787 444.86031584
3 3 197861763 1052911 532.14475806
4 4 191014876 680513 356.26178141
5 5 180716869 1109566 613.98031415
6 6 170718280 732517 429.07941669
7 7 159087445 760501 478.03960897
8 8 146274620 773008 528.46351609
9 9 141129459 569198 403.31622046
10 10 135440109 616809 455.41088571
11 11 134784419 742902 551.17795181
12 12 133756705 700715 523.87280324
13 13 96060333 379412 394.97260539
14 14 88286192 435617 493.41464405
15 15 82498740 495383 600.47341329
16 16 90225070 358919 397.80406931
17 17 81159168 352999 434.94654849
18 18 78004121 334153 428.37864938
19 19 59017259 229126 388.23558376
20 20 62905359 314623 500.15293610
21 21 38685809 146084 377.61650532
22 22 35030625 110792 316.27183357
23 M 15970 47 294.30181590
24 X 152228929 632103 415.23185123
25 Y 55317404 10 0.01807749
Cell types:
HAP1 HeLa MEF Patski
3194182 10713017 1 3
Sample: GSM2438426_ML4,human,unique.rds
# A tibble: 27,021,519 x 8
# Groups: chr_a [23]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 61887 62082 1 101667 101735 Nocadazole 20
2 1 61887 62082 1 247984 248051 Nocadazole 20
3 1 101667 101735 1 1885181 1885349 Nocadazole 54
4 1 124901 124934 1 96664199 96664266 Nocadazole 91
5 1 235158 235188 1 52253263 52253497 Asynchronous 120
6 1 562004 562081 1 20898624 20898764 Nocadazole 153
7 1 636630 636760 1 6425671 6425911 Nocadazole 157
8 1 636630 636760 1 27252279 27252419 Nocadazole 74
9 1 648845 648891 1 1517212 1517252 Nocadazole 159
10 1 648845 648891 1 4754301 4754455 Nocadazole 160
# ... with 27,021,509 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 249172978 2664364 1069.2829
2 2 243174534 1982115 815.0997
3 3 197861763 2015873 1018.8290
4 4 191011988 1128153 590.6190
5 5 180716869 2251626 1245.9412
6 6 170798397 1338128 783.4547
7 7 159094994 1457537 916.1426
8 8 146274593 1517530 1037.4529
9 9 141105245 1154848 818.4302
10 10 135448202 1197094 883.8021
11 11 134783335 1464853 1086.8206
12 12 133779100 1384026 1034.5607
13 13 96080185 680431 708.1908
14 14 88288101 858766 972.6860
15 15 82470913 980615 1189.0435
16 16 90208752 738362 818.5037
17 17 81171113 744759 917.5173
18 18 78004121 623718 799.5962
19 19 58879204 502206 852.9429
20 20 62905359 657318 1044.9316
21 21 38697772 291427 753.0847
22 22 35182925 214882 610.7565
23 X 154118408 1172888 761.0304
Cell types:
Asynchronous Nocadazole
9677605 16710710
Organism: mouse
Sample: GSM2254215_ML1,mouse,unique.rds
# A tibble: 4,002,891 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000983 3001047 1 4965798 4965885 MEF 1
2 1 3001122 3001293 1 3074714 3074770 Patski 2
3 1 3003353 3003418 1 4320235 4320402 MEF 3
4 1 3003486 3003575 1 3006173 3006412 MEF 4
5 1 3003486 3003575 1 3008062 3008094 Patski 5
6 1 3003604 3003815 1 3007753 3007894 Patski 6
7 1 3003604 3003815 1 4337484 4337520 Patski 7
8 1 3003944 3004012 1 4022994 4023131 Patski 8
9 1 3004055 3004111 1 9903838 9903888 MEF 9
10 1 3005547 3005760 1 4366159 4366227 Patski 10
# ... with 4,002,881 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192370575 298510 155.17445950
2 2 178961532 298348 166.71068730
3 3 156938025 398025 253.61922326
4 4 153294221 140135 91.41570966
5 5 148727398 303031 203.74927826
6 6 146528721 233740 159.51821486
7 7 142332981 193032 135.62000785
8 8 126224923 203117 160.91671531
9 9 121455460 198246 163.22526793
10 10 127491527 199774 156.69590341
11 11 118870753 193454 162.74314339
12 12 117016944 132611 113.32632307
13 13 117318086 166621 142.02499008
14 14 121795777 151282 124.20956106
15 15 100888736 172940 171.41655933
16 16 94873635 147998 155.99486622
17 17 91886447 150221 163.48548116
18 18 87598479 135896 155.13511370
19 19 58252297 92433 158.67700462
20 M 14403 36 249.94792752
21 X 166912961 193417 115.87895802
22 Y 37584000 24 0.06385696
Cell types:
MEF Patski
202759 3450173
Sample: GSM2254216_ML2,mouse,unique.rds
# A tibble: 2,929,110 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3003604 3003815 1 70492182 70492319 <NA> 2
2 1 3003812 3004012 1 3717382 3717465 Patski 3
3 1 3004324 3004563 1 21621468 21621554 Patski 4
4 1 3005547 3005760 1 67040987 67041061 Patski 5
5 1 3006173 3006309 1 3009141 3009232 Patski 6
6 1 3007305 3007389 1 6836946 6836980 Patski 7
7 1 3007753 3007894 1 15516931 15517005 MEF 10
8 1 3008375 3008408 1 3011419 3011451 MEF 11
9 1 3008412 3008485 1 3451673 3451726 Patski 12
10 1 3009056 3009103 1 3589463 3589516 Patski 13
# ... with 2,929,100 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192367954 217400 113.01258629
2 2 178961532 216137 120.77288207
3 3 156936036 275368 175.46511752
4 4 153201184 109521 71.48835090
5 5 148720774 213645 143.65511573
6 6 146530342 172419 117.66777969
7 7 142332839 148740 104.50153390
8 8 126265160 151005 119.59356009
9 9 121447043 147119 121.13839610
10 10 127493471 146113 114.60430001
11 11 118871165 145708 122.57640446
12 12 117026794 99054 84.64215468
13 13 117318982 121788 103.80928808
14 14 121795734 110786 90.96049292
15 15 100888668 127878 126.75159910
16 16 95021314 108288 113.96180019
17 17 91886612 112149 122.05151279
18 18 87599334 98157 112.05222177
19 19 58248179 68955 118.38138322
20 M 14403 9 62.48698188
21 X 166929063 138830 83.16706360
22 Y 86183943 41 0.04757267
Cell types:
MEF Patski
350996 2314028
Sample: GSM2254217_ML3,mouse,unique.rds
# A tibble: 741,760 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000984 3001047 1 23351683 23351757 MEF 1
2 1 3006173 3006309 1 3006531 3006563 MEF 2
3 1 3007393 3007454 1 4326789 4326851 Patski 3
4 1 3008354 3008408 1 4710734 4710973 Patski 4
5 1 3012619 3012668 1 5178289 5178348 <NA> 5
6 1 3013262 3013309 1 36929665 36929724 Patski 3
7 1 3014512 3014555 1 18533138 18533187 MEF 6
8 1 3028842 3028900 1 22733715 22733776 MEF 7
9 1 3032078 3032164 1 3048394 3048459 MEF 8
10 1 3035765 3035841 1 31976505 31976552 MEF 10
# ... with 741,750 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192369584 56693 29.4708752
2 2 178960181 55646 31.0940678
3 3 156937414 55988 35.6753680
4 4 153266009 34625 22.5914410
5 5 148729365 47085 31.6581732
6 6 146525804 42927 29.2965463
7 7 142323304 38728 27.2112851
8 8 126254719 38079 30.1604568
9 9 121414022 39131 32.2293911
10 10 127493829 38343 30.0743968
11 11 118869954 38668 32.5296668
12 12 116996617 30215 25.8255331
13 13 117284693 32219 27.4707630
14 14 120777208 29810 24.6818092
15 15 100886702 31822 31.5423137
16 16 94872481 28118 29.6376775
17 17 91880893 26514 28.8569246
18 18 87594240 26649 30.4232333
19 19 58218505 19262 33.0857002
20 M 14079 19 134.9527665
21 X 166772990 31175 18.6930749
22 Y 43187668 44 0.1018809
Cell types:
MEF Patski
399235 239268
Sample: GSM2254218_PL1,mouse,unique.rds
# A tibble: 9,055,515 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000748 3000812 1 17336484 17336681 Patski 1
2 1 3000816 3000985 1 5889797 5889855 Patski 2
3 1 3000816 3000985 1 6666639 6666751 Patski 3
4 1 3000816 3000985 1 108504418 108504593 Patski 1
5 1 3000816 3000985 1 166212738 166212800 Patski 4
6 1 3000983 3001118 1 3008062 3008094 Patski 5
7 1 3000983 3001047 1 47091788 47091885 Patski 6
8 1 3000987 3001047 1 3067986 3068071 MEF 7
9 1 3001798 3002017 1 4341744 4341842 Patski 8
10 1 3003213 3003265 1 3657464 3657537 MEF 9
# ... with 9,055,505 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192370810 715843 372.1162270
2 2 178962007 663246 370.6071535
3 3 156938493 917870 584.8597004
4 4 153294811 301060 196.3928185
5 5 148732122 650775 437.5483865
6 6 146535828 537661 366.9143631
7 7 142338970 382479 268.7099675
8 8 126287205 443059 350.8344333
9 9 121449203 424215 349.2941819
10 10 127493829 485796 381.0349127
11 11 118875997 399061 335.6951866
12 12 117026963 319604 273.1028746
13 13 117320155 365252 311.3292852
14 14 121795777 344762 283.0656436
15 15 100890015 379861 376.5100045
16 16 95009733 349307 367.6539118
17 17 91885487 322803 351.3101041
18 18 87600284 315553 360.2191518
19 19 58252249 216572 371.7830706
20 M 14403 133 923.4187322
21 X 166934731 520441 311.7631645
22 Y 90041618 162 0.1799168
Cell types:
HAP1 HeLa MEF Patski
9 6 1146613 7908776
Sample: GSM2254219_PL2,mouse,unique.rds
# A tibble: 16,115,940 x 8
# Groups: chr_a [22]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000194 3000290 1 3380053 3380083 Patski 1
2 1 3000194 3000356 1 28278273 28278326 Patski 2
3 1 3000748 3000812 1 3036826 3036882 Patski 3
4 1 3000748 3000812 1 4321086 4321202 Patski 4
5 1 3000748 3000812 1 4339680 4339919 Patski 5
6 1 3000748 3000812 1 21180408 21180507 Patski 6
7 1 3000816 3000985 1 4223507 4223574 Patski 7
8 1 3000816 3000985 1 15453757 15453795 MEF 8
9 1 3000983 3001047 1 6537085 6537185 MEF 10
10 1 3003212 3003265 1 3034166 3034210 MEF 11
# ... with 16,115,930 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192371364 1235406 642.1984927
2 2 178962532 1196485 668.5673178
3 3 156938737 1500226 955.9309758
4 4 153306207 560631 365.6936082
5 5 148732157 1204207 809.6480440
6 6 146536084 956644 652.8385186
7 7 142338970 769031 540.2814141
8 8 126291290 820960 650.0527471
9 9 121494312 787839 648.4575179
10 10 127493829 830169 651.1444566
11 11 118876754 778814 655.1440663
12 12 117027004 558245 477.0223802
13 13 117319628 644301 549.1843189
14 14 121796062 598152 491.1094745
15 15 100888736 698341 692.1892648
16 16 94948659 604074 636.2111970
17 17 91886251 613980 668.1957239
18 18 87600284 544631 621.7228702
19 19 58248233 392717 674.2127268
20 M 14492 202 1393.8724814
21 X 167622474 820714 489.6205028
22 Y 90002613 171 0.1899945
Cell types:
HAP1 HeLa MEF Patski
82 44 1971223 14142703
Sample: GSM2438426_ML4,mouse,unique.rds
# A tibble: 3,156,550 x 8
# Groups: chr_a [20]
chr_a start_a end_a chr_b start_b end_b celltype cell_index
<chr> <int> <int> <chr> <int> <int> <chr> <int>
1 1 3000983 3001118 1 46187073 46187119 Patski 1
2 1 3003486 3003575 1 3007753 3007893 Patski 2
3 1 3003486 3003600 1 3010457 3010499 Patski 3
4 1 3003486 3003575 1 6887703 6887841 <NA> 4
5 1 3003812 3004051 1 3266448 3266508 Patski 6
6 1 3007393 3007461 1 3012057 3012248 Patski 8
7 1 3008104 3008339 1 3008412 3008479 Patski 9
8 1 3008412 3008485 1 3009117 3009232 Patski 10
9 1 3008691 3008930 1 39786341 39786393 Patski 11
10 1 3009056 3009103 1 5662792 5662882 Patski 12
# ... with 3,156,540 more rows
Chromosome summaries:
chromosome length count per_100kb
1 1 192370540 232374 120.79500
2 2 178961681 234286 130.91406
3 3 156938025 296009 188.61522
4 4 153271232 93474 60.98600
5 5 148727392 218531 146.93393
6 6 146529099 186966 127.59650
7 7 142330101 151370 106.35136
8 8 126221514 165131 130.82635
9 9 121445094 163369 134.52087
10 10 127492417 155766 122.17668
11 11 118874181 167034 140.51327
12 12 117017815 125093 106.90082
13 13 117317002 131356 111.96672
14 14 121779385 121738 99.96602
15 15 100879823 135975 134.78909
16 16 94866594 116172 122.45828
17 17 91886144 115494 125.69251
18 18 87599626 107904 123.17861
19 19 58247109 96674 165.97219
20 X 167488146 141834 84.68301
Cell types:
Patski
2729322
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