Returns a data.table showing counts of regions from the query that overlap with each bin. In other words, where on which chromosomes are the ranges distributed? You must provide binned regions. Only the midpoint of each query region is used to test for overlap with the bin regions.
calcChromBins(query, bins)A GenomicRanges or GenomicRangesList object with query regions
Pre-computed bins (as a GRangesList object) to aggregate over; for example, these could be genome bins
A data.table showing where on which chromosomes ranges are distributed.
chromSizes = getChromSizes("hg19")
genomeBins = getGenomeBins(chromSizes)
chromDistribution = calcChromBins(vistaEnhancers, genomeBins)
#> Finding overlaps...
#> Setting regionIDs...
#> Combining...
vistaSftd = GenomicRanges::shift(vistaEnhancers, 100000)
vistaSftd2 = GenomicRanges::shift(vistaEnhancers, 200000)
calcChromBins(vistaEnhancers, GRangesList(vistaSftd, vistaSftd2))
#> Finding overlaps...
#> Setting regionIDs...
#> Combining...
#> regionID chr start end withinGroupID regionGroupID N
#> 1: 51 chr1 83410681 83411769 51 1 1
#> 2: 100 chr1 213598113 213601134 100 1 1
#> 3: 115 chr10 36072893 36075932 115 1 1
#> 4: 143 chr10 102547082 102548985 143 1 1
#> 5: 192 chr11 31785358 31786884 192 1 1
#> 6: 306 chr14 29960530 29962348 306 1 1
#> 7: 437 chr16 54349595 54351153 437 1 1
#> 8: 444 chr16 54679727 54680655 444 1 1
#> 9: 629 chr2 59202072 59203380 629 1 1
#> 10: 636 chr2 59303218 59304548 636 1 1
#> 11: 663 chr2 66397528 66399214 663 1 1
#> 12: 716 chr2 146797739 146798645 716 1 1
#> 13: 739 chr2 164449677 164451112 739 1 1
#> 14: 788 chr20 39472457 39475024 788 1 1
#> 15: 996 chr5 92526547 92528433 996 1 1
#> 16: 1070 chr6 98361650 98363117 1070 1 1
#> 17: 1072 chr6 98462400 98463804 1072 1 1
#> 18: 1131 chr7 35459005 35459854 1131 1 1
#> 19: 1170 chr7 114395110 114396373 1170 1 1
#> 20: 1316 chrX 25015383 25018272 1316 1 1
#> 21: 1383 chr1 63664283 63665717 44 2 1
#> 22: 1577 chr12 103571348 103572610 238 2 1
#> 23: 1638 chr14 28598564 28600621 299 2 1
#> 24: 1643 chr14 29910886 29913340 304 2 1
#> 25: 1777 chr16 54523421 54524336 438 2 1
#> 26: 1958 chr2 58948341 58950140 619 2 1
#> 27: 2057 chr2 147333971 147334751 718 2 1
#> 28: 2409 chr6 98461650 98463117 1070 2 1
#> 29: 2514 chr7 115313552 115314543 1175 2 1
#> 30: 2636 chr9 128606148 128607653 1297 2 1
#> regionID chr start end withinGroupID regionGroupID N