Generate a fragment distance vector for your digested DNAString object
Source:R/FROG_nonpal.R
FROG_nonpal.RdGenerate a fragment distance vector for your digested DNAString object
Arguments
- my_DNA,
That's your DNAString you aim to digest
- pattern1,
The non-PALINDROMIC sequence pattern the restriction enzyme 1 recognizes
- pattern2,
OPTIONAL: The non-PALINDROMIC nucleotide sequence pattern the restriction enzyme 2 recognizes
Examples
my_DNA<-gen_DNA(1000)
pattern1<-'ATGCTGATT'
pattern2<-'CGTGACTGGA'
FROG_pal(my_DNA, pattern1, pattern2)
#> [1] 999
library(BSgenome.Hsapiens.UCSC.hg38)
chr1_Hsapiens<-BSgenome.Hsapiens.UCSC.hg38$chr1
FROG_pal(chr1_Hsapiens, pattern1)
#> [1] 393921 229892 221212 54620 1299822 223607 214061 331081
#> [9] 894139 311973 342579 226949 111959 164245 49073 310941
#> [17] 34052 37 37 1232218 129016 20509 284141 75784
#> [25] 590758 30060 544156 276241 559607 1022149 22843 16126
#> [33] 300966 73688 1142490 124693 289623 218806 22198 26348
#> [41] 33758 62814 253811 457776 208880 437959 499275 23283
#> [49] 97448 57479 121633 73120 147813 5650 87863 195362
#> [57] 83928 765264 21747 132445 392453 6277 6305 568780
#> [65] 160931 499 265952 205445 247810 81293 307761 49567
#> [73] 78491 227456 120608 28076 170166 27948 30180 15119
#> [81] 12364 192143 10497 105955 179343 213712 135770 83897
#> [89] 16645 545862 212824 23299 64133 6581 87651 24331
#> [97] 99761 295136 310449 1031053 78849 266506 532746 37507
#> [105] 231605 365007 400273 23971 323473 264440 186910 53325
#> [113] 49303 23944 150748 104904 245699 869525 478495 504552
#> [121] 36727 599282 752239 172457 218526 31499 32321 265443
#> [129] 194350 153064 700696 601918 6672 131498 129561 21438
#> [137] 183864 208142 164684 1113243 25915 643192 175781 750035
#> [145] 99793 290570 120829 135995 183466 81644 31335 8474
#> [153] 286063 799316 458958 19359 2090 39737 259167 152564
#> [161] 208839 82728 141490 256761 165557 32925 277171 243627
#> [169] 292628 11799 258244 7293 142498 98326 151225 41118
#> [177] 31443 128561 242831 117632 600031 48617 66594 97606
#> [185] 60555 3376 161059 486048 62131 13198 34841 29561
#> [193] 125683 109877 963849 59076 5718 221916 56291 106493
#> [201] 727219 164802 307888 103341 156098 497707 139111 65068
#> [209] 151525 215256 899754 49243 78503 202874 490117 5811
#> [217] 11252 9094 52019 190730 187280 59326 47048 58779
#> [225] 189230 82231 394823 247054 451652 978131 88546 224645
#> [233] 227742 230380 291820 247779 341220 332735 112295 102874
#> [241] 34206 205747 216941 724495 70538 264032 257289 103030
#> [249] 95696 67726 1594 3031 48377 142870 33839 99426
#> [257] 530982 185230 57157 58136 13074 297037 70370 21128
#> [265] 386712 238506 71391 278248 109460 95595 36097 53626
#> [273] 106892 160823 49706 4856 7311 32847 29770 495627
#> [281] 102160 10943 90902 160030 32028 175370 175301 109520
#> [289] 346743 164616 30695 148104 37556 18305 162320 61794
#> [297] 372660 90876 290721 77372 73582 108020 139488 282127
#> [305] 35309 7548 41155 467249 117152 139875 17036 86785
#> [313] 112196 48802 326253 46824 112440 55461 37669 4448
#> [321] 608988 54024 463203 283951 60171 708583 40359 72075
#> [329] 91024 26845 70213 134483 40522 65203 73356 344567
#> [337] 28675 44635 535266 89265 28149 111276 81374 271222
#> [345] 49449 131948 140343 51128 160882 273679 104737 246575
#> [353] 37444 292779 109277 218435 27498 12417 98239 184467
#> [361] 125933 26808 280607 199306 8914 119414 78295 32991
#> [369] 9001 57296 118633 77830 94245 167134 109258 245020
#> [377] 608084 54829 208197 89790 12833 336696 213963 126350
#> [385] 18723 562634 81233 187562 163166 34439 321773 39016
#> [393] 191182 184978 5171 131372 170150 46155 78260 32680
#> [401] 48604 384872 30806 367642 43185 177336 189422 18792
#> [409] 313 153617 372621 196696 78604 571654 96406 2985
#> [417] 189459 131877 120728 3347 184331 41727 327 109209
#> [425] 12035 151131 211574 292757 380139 94978 26408 4587
#> [433] 2689 137588 28270 23317 69088 120917 97715 31996
#> [441] 6234 20955 119403 14972 74242 73215 45977 228783
#> [449] 154176 49267 30081 101425 105864 29551 84123 301393
#> [457] 155026 2963 90126 389671 9967 265228 115307 16569
#> [465] 96862 289028 228368 15340 4952 102712 284847 544402
#> [473] 113752 45506 7516 30637 240986 210748 95182 179556
#> [481] 679785 92501 181012 126807 93325 220723 90084 286179
#> [489] 50137 154138 184450 133563 82429 44177 240164 69224
#> [497] 25878 703587 21 26552 631942 13530 5429 102360
#> [505] 348024 76540 44574 570641 476210 244512 24859 400574
#> [513] 228859 536052 47928 11418 23948 236447 146739 15581
#> [521] 155909 1740 31411 27855 179422 22740 13760 208083
#> [529] 425515 115 17300 58013 188920 12438 4661 83383
#> [537] 37961 344573 77212 95016 130574 24885 325942 22205
#> [545] 16216 40166 223177 398102 136682 234500 222274 8869
#> [553] 283842 24862 391819 103984 241280 226434 337598 219718
#> [561] 119510 13603 32724 21183 33811 67413 9857 194435
#> [569] 264761 193465 118389 37267 33535 23984 41448 836814
#> [577] 215145 174284 28456 87667 207727 248832 30518 19025
#> [585] 19502 16102 244129 5337 28232 16141 3068 353815
#> [593] 29936 3005 116664 472525 176975 52938 50189 212528
#> [601] 46571 6547 130522 363573 5253 69539 13414 69487
#> [609] 183330 40197 63029 37212 491159 541235 83865 104641
#> [617] 367454 132647 55272 47762 205040 356125 103929 37109
#> [625] 19175 206006 108677 170191 341993 52153 27951 159004
#> [633] 352865 338194 359923 313375 11589 37949 12276 124295
#> [641] 124347 518848 18551 107852 15307 109012 292832 84567
#> [649] 79966 262248 609809 44283 193033 364091 96590 522633
#> [657] 349348 181562 30160 116140 163485 71349 655 492489
#> [665] 287606 60252 108651 113791 149068 266798 173571 96859
#> [673] 150788 154310 93066 227419 175174 48350 123835 9638
#> [681] 93963 115729 112142 48997 35417 306440 93546 80016
#> [689] 4848 197769 23464 68625 31291 298875 218453 161327
#> [697] 71442 175066 374371 465283 3842778 4081 4957 3916
#> [705] 18317684 127548 698081 379311 351039 85158 65644 400362
#> [713] 75676 137582 65367 352674 341773 54810 30487 349772
#> [721] 79412 44630 168955 108124 88103 66025 56988 40887
#> [729] 162784 174497 298797 384695 162681 71871 67779 583935
#> [737] 290489 104838 695960 192700 78618 84923 296477 448715
#> [745] 49956 123744 247090 17272 372254 100025 12766 78778
#> [753] 18988 567631 439292 87476 132087 327219 73025 315076
#> [761] 418439 81990 6687 11863 2076 8299 5521 694620
#> [769] 170300 93370 470717 114241 447858 259538 164620 78631
#> [777] 5074 15299 102255 21109 36971 353360 209212 310400
#> [785] 81261 184310 119120 32748 7574 103534 49654 155571
#> [793] 306374 304040 115623 75160 92483 401196 170523 289568
#> [801] 149990 267985 324 154604 408499 111763 7214 361563
#> [809] 219724 6047 80285 173644 148198 118845 412408 23980
#> [817] 141351 172434 458376 500919 108221 328196 341295 43663
#> [825] 664997 100799 37881 341608 381616 56765 70698 211796
#> [833] 328 61979 648611 381350 62456 65461 88178 42289
#> [841] 1469 85133 111278 375370 47365 84999 225940 60492
#> [849] 246720 17599 56960 784 126650 59209 32587 203668
#> [857] 96473 30043 57309 469 157429 178503 259233 58324
#> [865] 44331 63851 25092 56178 132014 121013 87427 319273
#> [873] 27075 368528 209388 693417 97024 243892 2479 269805
#> [881] 65203 88147 348 133721 274712 109517 151371 85499
#> [889] 448818 296379 144522 9590 70669 94312 36913 49441
#> [897] 95388 381079 300628 130163 34347 218281 262068 136958
#> [905] 331179 41136 39578 329928 6169 148939 424212 6982
#> [913] 21286 388499 565931 92416 79129 468473 38227 73955
#> [921] 97100 38149 82416 11303 1214 17861 19672 30522
#> [929] 228081 245101 14939 102402 208424 32720 7475 1528
#> [937] 32407 122992 319568 129852 486355 208805 195856 192654
#> [945] 448461 200695 169274 2959 406337 18097 52268 219717
#> [953] 35538 87037 31990 45751 411829 204023 108590 81065
#> [961] 22640 96585 35747 411485 68273 25641 30759 275081
#> [969] 187158 131254 93245 36098 47430 190667 116282 79633
#> [977] 21820 47844 123104 91213 166545 125010 523099 25292
#> [985] 302719 1112 54432 137804 70719 14574 66853 360170
#> [993] 91016 549181 17775 318297 40532 2265 56337 171604
#> [ reached getOption("max.print") -- omitted 362 entries ]