Generate a fragment distance vector for your digested DNAString object
Source:R/FROG_mix.R
FROG_mix.RdGenerate a fragment distance vector for your digested DNAString object
Arguments
- my_DNA,
That's your DNAString you aim to digest
- pattern1,
The palindromic sequence pattern the restriction enzyme 1 recognizes
- pattern2,
The non-PALINDROMIC nucleotide sequence pattern the restriction enzyme 2 recognizes
Examples
my_DNA<-gen_DNA(1000)
pattern1<-'CATATG'
pattern2<-'CGTGACTGGA'
FROG_pal(my_DNA, pattern1, pattern2)
#> [1] 999
library(BSgenome.Hsapiens.UCSC.hg38)
#> Loading required package: GenomeInfoDb
#> Loading required package: BiocGenerics
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#> Attaching package: ‘BiocGenerics’
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#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#> tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
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#> reduce
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#> windows
#> Loading required package: BSgenome
#> Loading required package: GenomicRanges
#> Loading required package: Biostrings
#> Loading required package: XVector
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#> Attaching package: ‘XVector’
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#> compact
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#> strsplit
#> Loading required package: rtracklayer
chr1_Hsapiens<-BSgenome.Hsapiens.UCSC.hg38$chr1
FROG_pal(chr1_Hsapiens, pattern1, pattern2)
#> [1] 11484 14896 94 1052 8944 2809 3333 1902 1418 214 1978 599
#> [13] 15 802 1394 3492 784 711 4765 2617 1299 7774 1530 2330
#> [25] 285 2992 6284 8574 2398 5704 5079 265 1991 184 3184 4936
#> [37] 164 650 1994 2121 20944 13343 402 700 18794 1613 3166 14899
#> [49] 94 1052 8941 51628 2154 5552 4625 2405 5685 5078 265 1991
#> [61] 184 3186 4936 164 654 1994 50530 2156 984 4545 8136 574
#> [73] 676 2850 14659 1328 7850 1148 4284 3432 12239 6927 2754 976
#> [85] 1319 2094 1293 3310 772 3458 541 2270 7263 285 441 312
#> [97] 421 3154 3695 3808 11210 4935 164 654 1996 2121 23540 13326
#> [109] 402 700 18789 57094 574 676 2839 15496 1328 7850 1148 4276
#> [121] 9302 12242 6911 2756 976 1319 2094 1293 3311 782 2685 541
#> [133] 2270 7260 285 441 312 421 3154 3693 3805 11216 4936 164
#> [145] 654 1995 2088 30326 13310 545 700 21988 4802 1361 3836 7962
#> [157] 670 686 686 51 385 2431 3726 510 448 454 2590 991
#> [169] 804 3395 8448 936 4055 3645 14480 2488 4614 2567 111 3672
#> [181] 6496 5473 3161 2608 2163 2609 12897 4486 16211 27393 24494 493
#> [193] 16349 1753 1147 39862 22992 271 22320 8232 20291 19559 7339 23124
#> [205] 33021 771 1166 1072 2085 1857 570 984 10817 36061 8753 21649
#> [217] 31781 13460 9643 2286 900 4649 5746 2100 22139 99867 1912 23779
#> [229] 5029 7755 38691 3037 14226 5612 16361 10051 14065 14885 6074 20062
#> [241] 1811 7972 3912 18223 35322 1722 10044 38170 2031 14721 5749 1619
#> [253] 13836 3090 189 4251 17064 21734 12231 6328 20769 5602 190 5982
#> [265] 32197 7439 702 1118 4127 30830 7154 21174 9645 2256 12782 10689
#> [277] 45498 36889 22039 924 14325 26412 17207 19643 20914 10711 6750 981
#> [289] 13084 70679 6704 4547 8481 285 1364 5807 2155 8355 2032 11305
#> [301] 359 42 94 28667 11530 997 15551 10196 8731 8827 3149 77567
#> [313] 8862 12123 679 1478 16363 7174 178 132 198 9307 8892 3192
#> [325] 735 34840 18347 15777 887 1246 58818 887 1406 1932 1653 1495
#> [337] 726 1456 1932 1813 1698 845 652 1797 9918 2775 26628 208
#> [349] 23454 121 1829 277 17610 31293 117 3444 274 6365 5287 6872
#> [361] 372 77 193 371 6519 6722 8332 6841 11862 776 5112 10057
#> [373] 13474 6579 439 3801 17180 140 5673 6618 9054 3805 193 18674
#> [385] 28409 14678 1090 5760 6053 4021 22996 4934 7154 20468 4924 2457
#> [397] 7941 7688 1174 2831 2861 28911 4326 7866 2101 5983 1547 285
#> [409] 8511 9807 4363 36 16148 15474 1400 10453 182 149 302 161
#> [421] 14101 489 291 170 807 5620 16573 23916 100 12964 2059 2488
#> [433] 3979 5413 9379 6041 223 40 255 6683 1781 9753 4405 13365
#> [445] 1662 7201 2228 7686 5757 13058 10546 17385 24007 10755 8329 78
#> [457] 13576 445 561 25 19032 142 232 20553 10357 1972 7155 10529
#> [469] 807 12841 40815 1229 37269 295 10151 8348 18521 17653 8144 6964
#> [481] 6298 3243 4801 583 3604 3642 3674 1929 3229 11663 92 330
#> [493] 2867 1326 228 7445 468 312 211 4517 5392 6425 13458 10412
#> [505] 1142 5879 7880 285 8617 2934 21799 10928 270 12116 1982 526
#> [517] 689 725 9125 9335 5932 18585 4015 1698 4689 257 12007 3194
#> [529] 1004 10975 11803 582 19135 285 4464 50 9394 713 36071 6150
#> [541] 975 7379 111 430 5557 14474 77 5642 1322 2975 491 1203
#> [553] 1616 3611 599 7790 15700 3384 2399 7460 578 397 754 1790
#> [565] 8278 2806 4314 2669 4447 9833 211 2330 166 542 3809 2980
#> [577] 2249 60 5685 300 17758 1174 3594 1247 7882 7403 1351 13038
#> [589] 2197 1528 10676 1046 352 11382 4616 5146 4788 22 202 4000
#> [601] 12374 1083 8800 3969 3612 526 221 54 1091 666 1687 6589
#> [613] 7085 4843 2416 264 306 10824 7215 917 367 6295 15590 2281
#> [625] 8307 395 2908 348 1451 23113 1310 338 4118 2286 275 711
#> [637] 4313 3448 666 3226 2878 2842 6688 5188 6234 444 285 16499
#> [649] 23273 2895 6345 8053 63 6244 773 460 3455 2108 12309 16896
#> [661] 2975 1585 13601 903 142 7324 962 11047 8743 15232 88 4329
#> [673] 3003 2482 5945 9782 4855 8942 3955 10 1976 1490 3701 2863
#> [685] 2594 393 11093 4647 288 1480 534 4199 15388 381 6570 3155
#> [697] 3852 2991 4353 5283 1151 285 786 4577 180 8444 2614 6351
#> [709] 706 239 575 6949 14 9466 1481 7336 1301 2660 7512 760
#> [721] 2666 90 12454 20 20 20 84 20 60 60 6738 5792
#> [733] 15159 30190 653 4737 2451 3767 889 2377 4653 2946 7492 1642
#> [745] 2385 1863 3601 140 336 4051 3123 4366 1142 5871 4806 260
#> [757] 6283 9509 3712 4185 33 2443 345 1428 2129 4296 4690 2110
#> [769] 691 1238 2685 13650 10734 13899 2875 927 8007 2153 7645 2793
#> [781] 8420 3970 1301 19 902 1204 3300 118 5531 1901 2045 9170
#> [793] 588 7477 921 309 112 86 11621 2671 2701 595 3400 2873
#> [805] 4855 1874 958 6186 19 1768 187 3609 2030 2540 1528 1390
#> [817] 4233 3369 3192 3505 135 15602 2825 2086 2878 36 629 13234
#> [829] 603 3039 6806 5429 1973 16521 1563 906 581 17915 394 1390
#> [841] 10209 3833 1034 111 4218 11693 1631 10441 2670 3627 41 2553
#> [853] 15265 5177 7852 6528 12475 12605 3053 6305 18 120 2987 3563
#> [865] 16499 968 4503 5108 2938 37 3479 3607 971 1971 1111 9882
#> [877] 5947 6782 6313 4335 1951 4564 5487 867 99 14762 2677 266
#> [889] 2996 155 6521 3074 3276 856 818 1145 1835 575 507 2047
#> [901] 814 119 2498 734 3876 1807 4651 5109 1574 469 4418 2092
#> [913] 1268 10104 2448 2224 3694 8657 13435 7367 4049 10558 1649 2284
#> [925] 3176 2838 2457 3475 118 26946 15103 1540 2901 72 6339 75
#> [937] 60 7578 201 3745 145 2328 421 265 422 12725 1999 285
#> [949] 1148 14319 28620 131 10828 15083 3163 6549 16261 870 325 6021
#> [961] 531 53 985 1837 4035 18922 1321 9796 5951 3232 3841 4469
#> [973] 618 25840 758 12630 7485 183 64 2762 68 90 46 9615
#> [985] 20204 11792 4897 7304 6537 24054 1835 32 18958 305 21688 3728
#> [997] 2961 8317 22455 41915
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