R/feature-plots.R
calcFeatureDistRefTSS.RdGiven 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
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#> [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
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#> [105] 250663 235446 7889 -58379 137201 118248 -3292 -25253
#> [113] 62326 -9918 -44051 -142920 -242823 -17247 -1033 144685
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#> [537] 208013 184011 175610 164286 162308 122995 66548 -351984
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#> [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
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#> [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
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#> [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
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