R/feature-plots.R
calcFeatureDistRefTSS.Rd
Given a query GRanges object and an assembly string, this function will grab
the TSS list for the given reference assembly and then calculate the distance
from each query feature to the closest TSS. It is a wrapper of
calcFeatureDist
that uses built-in TSS features for a reference
assembly
calcFeatureDistRefTSS(query, refAssembly)
A GenomicRanges or GenomicRangesList object with query regions
A character vector specifying the reference genome
assembly (*e.g.* 'hg19'). This will be used to grab chromosome sizes with
getTSSs
.
A vector of distances for each query region relative to TSSs.
calcFeatureDistRefTSS(vistaEnhancers, "hg19")
#> [1] 179984 -44796 -61083 124112 98559 75215 4835 -68758
#> [9] 76457 -27740 27159 -1082 -43169 17261 -48451 -115948
#> [17] -144753 -150975 -224209 -280216 -289809 -307424 132123 76051
#> [25] 33524 -3941 -4721 -36649 -119622 129581 -117531 -146246
#> [33] -210206 259944 -47785 239100 176399 243566 272102 144285
#> [41] 136424 -120317 -194404 -215195 123058 -785945 -892031 -893170
#> [49] 1243797 1212114 1153608 1119014 1103928 1053168 586065 -1815
#> [57] -10164 -28202 -28202 -234869 -271636 -314591 -390158 -609705
#> [65] 612849 571726 554219 533596 502482 462995 307490 273442
#> [73] 222251 -123595 99128 -423896 -41404 -301145 79102 -68286
#> [81] -150815 -216975 584651 501091 326320 -95781 -113486 -144388
#> [89] -148677 -176071 -107936 -48330 -64715 -138561 169570 39405
#> [97] -647981 -9972 -29336 -275035 -374157 -148914 -176199 37687
#> [105] 250663 235446 7889 -58379 137201 118248 -3292 -25253
#> [113] 62326 -9918 -44051 -142920 -242823 -17247 -1033 144685
#> [121] 18956 -267424 71417 -26234 22699 -3438 -323047 -366243
#> [129] -629736 -796638 -922794 -941318 1007120 -502751 -9315 -68049
#> [137] 25867 -22792 -83454 -85426 80112 75933 47325 -51984
#> [145] -56564 10340 18820 84505 63005 8060 2565 -918698
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#> [161] -60101 43035 3854 -195065 236338 -55924 -39930 -442788
#> [169] 433131 157814 -92089 -95164 -137211 -205979 70138 -17716
#> [177] -37763 14527 -27705 -170971 -188334 -453709 -490578 443018
#> [185] 322440 317793 306286 256244 210024 28596 -92175 147817
#> [193] 47613 16501 -150089 -213438 259063 7619 -52236 35356
#> [201] 64681 162452 57986 -37979 -62171 410793 -2569 186451
#> [209] 74053 -627792 141479 -112663 106305 -107102 -110916 47690
#> [217] -106696 -177987 -270339 -549244 742176 689798 574951 551817
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#> [233] -146976 69549 344975 -168896 5491 -19791 -54900 -26572
#> [241] -69014 -23998 33085 185560 -1885 -2878 -29970 -256924
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#> [257] -851025 717619 666221 647322 646951 377733 184892 184865
#> [265] 139438 107077 94225 14268 -227748 -253155 -328389 -331244
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#> [337] 269653 -51705 467181 350696 271188 -81920 -265597 -80776
#> [345] 51953 -93648 -95021 -112196 201489 175206 151852 44724
#> [353] 21070 -120112 -128884 -260118 53881 398643 -214781 -215671
#> [361] -1057 156545 -117892 32043 -1580 19019 157561 -54668
#> [369] -561955 197443 -65702 277414 -480359 1202899 1189731 863110
#> [377] 735020 488636 383316 190373 163026 -43742 467937 -181021
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#> [489] 182850 81769 -11624 252480 -316124 -335991 201456 150632
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#> [505] -45864 423885 -54203 -100310 -23473 -30486 -141701 -168431
#> [513] -7892 8255 16420 -12344 33767 1212 -46405 -155
#> [521] -31146 27706 -19255 147920 47252 -29217 -835306 782063
#> [529] -55520 -24855 -24855 -53397 -99962 -196095 274064 239125
#> [537] 208013 184011 175610 164286 162308 122995 66548 -351984
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#> [609] 80129 -72949 137247 100212 61611 40195 417441 162009
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#> [633] -711110 -731211 -734331 -735376 -835943 -837427 -1008773 -1072782
#> [641] 1034017 890613 884826 882803 832919 781705 774164 724403
#> [649] 702795 641844 556188 482492 462890 427643 338696 280666
#> [657] 263607 -14837 -75271 82799 70898 8527 362212 262340
#> [665] 149407 -89653 -264827 -391919 342551 209080 195150 -212625
#> [673] -31897 50104 -20770 -195703 -207103 -417223 -439708 -556924
#> [681] -664869 -708282 -711339 -932759 895220 894327 822687 802707
#> [689] 784303 735026 423755 338645 283608 216721 170967 18396
#> [697] -45646 -43245 -70799 209915 195997 508097 -66012 -255833
#> [705] -263410 -266942 377083 93191 81117 -58420 -720954 -775929
#> [713] -1130833 -1407428 -1410639 -1416045 -1516489 1467724 1429182 1341106
#> [721] 1312052 1267715 798220 795291 613497 539401 471766 436245
#> [729] 207113 -198828 -307630 -368452 252353 213852 108075 45315
#> [737] 69374 410969 242127 141571 17789 -65018 -69497 -251768
#> [745] 164268 -41883 12083 954 -6999 -8879 104395 126921
#> [753] 123876 71474 3094 -5626 112859 7900 -369292 -5823
#> [761] -558291 653362 -323119 261871 -7007 -223537 -280134 82953
#> [769] 11534 -494320 113284 5405 7447 -45976 -139118 -124813
#> [777] 67930 5378 950 -27020 -47612 -286266 736425 454494
#> [785] -16741 -29859 -50047 -55861 -144708 -155295 -166090 81852
#> [793] 330 311282 35673 -148221 450722 337369 -424821 -579640
#> [801] -849993 841183 43452 -240483 -25064 60334 -185013 2769
#> [809] -5481 -41530 -32284 3309 1389 -8889 -11343 22439
#> [817] 9807 5622 9681 -764864 498020 316509 345064 290708
#> [825] 272923 161393 155735 -16903 -1429 -85988 8776 -219
#> [833] -46959 -35464 -777462 -913612 761003 606643 598230 580329
#> [841] 533136 445652 378798 355005 341639 185322 132916 124968
#> [849] 59066 41298 440406 773299 -270191 -569186 431818 290740
#> [857] 254019 -318371 -383337 -403203 357504 297163 122184 78066
#> [865] 80208 60889 -1094 -254929 -269039 -624151 -629818 621842
#> [873] 613978 612598 408415 233848 46772 -27236 -58842 -79685
#> [881] -165747 -185887 -202273 87009 42735 547439 420767 -336052
#> [889] -117276 123578 -67159 -530238 -192602 115228 192285 175088
#> [897] 72236 41245 586072 534314 476166 359060 28342 -640032
#> [905] -488635 4317 -96578 168865 45373 3292 -106656 -453710
#> [913] -97249 -101533 -243572 173529 -118362 88666 69822 27108
#> [921] 32805 -15271 -106935 -271815 -352957 -473480 -568402 644198
#> [929] 509169 397443 -66992 -459724 -203370 -215862 -1930 158441
#> [937] 214212 8923 -17188 168167 -33284 14788 1863095 -225393
#> [945] -319069 416144 413422 408984 397763 369364 83478 136692
#> [953] 198690 -9 343073 209950 196945 -29466 -176409 -281930
#> [961] 15221 4437 -233 -5604 -86044 24372 16514 -103691
#> [969] -52440 -375047 396369 324499 -127417 20199 -349529 -474031
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#> [985] -640001 -1021620 -1086398 1114782 1090328 977559 886899 882814
#> [993] 776518 698551 603610 491552 441068 392332 382175 175919
#> [1001] 106700 -150311 -128614 -203253 192326 96331 -294824 148717
#> [1009] -160321 -247290 -568176 -599664 -624864 -8104 12515 12166
#> [1017] 146451 -6647 -13978 -541229 -303571 -467280 508351 382694
#> [1025] 298170 184982 39960 8419 385656 -129025 -170572 -182939
#> [1033] 152329 107282 -13537 -1644 29163 29163 106428 -660366
#> [1041] 25418 11153 -80682 -168670 -244967 -294637 303066 -334131
#> [1049] 147749 -611422 248537 -77646 79087 76743 -9288 -119061
#> [1057] 199204 -110875 128217 -4201 -290273 -362754 435968 54060
#> [1065] -172582 -23685 -218336 -385421 -482423 -531291 -548646 -632009
#> [1073] -652103 -731538 -761441 -773954 709490 562444 468304 450520
#> [1081] 379304 286612 275882 -29937 -216529 -61397 102284 261952
#> [1089] 98323 127665 51139 49210 -155789 -100423 55757 -514117
#> [1097] -129578 6805 4041 -798249 295044 579730 524308 -349134
#> [1105] -317825 270694 -3394 -6760 -177510 -193871 -258396 227302
#> [1113] 174015 -267139 398766 271088 53258 -51761 -10733 -6717
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#> [1145] 68276 -335973 -533718 -639020 714928 705518 616198 493426
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