Creates a cartesian grid two-dimensional iterator that can be used by any function that accepts an iterator argument.
giterator.cartesian_grid(
intervals1 = NULL,
expansion1 = NULL,
intervals2 = NULL,
expansion2 = NULL,
min.band.idx = NULL,
max.band.idx = NULL
)one-dimensional intervals
an array of integers that define expansion around intervals1 centers
one-dimensional intervals. If 'NULL' then 'intervals2' is considered to be equal to 'intervals1'
an array of integers that define expansion around intervals2 centers. If 'NULL' then 'expansion2' is considered to be equal to 'expansion1'
integers that limit iterator intervals to band
A list containing the definition of cartesian iterator.
This function creates and returns a cartesian grid two-dimensional iterator that can be used by any function that accepts an iterator argument.
Assume 'centers1' and 'centers2' to be the central points of each interval from 'intervals1' and 'intervals2', and 'C1', 'C2' to be two points from 'centers1', 'centers2' accordingly. Assume also that the values in 'expansion1' and 'expansion2' are unique and sorted.
'giterator.cartesian_grid' creates a set of all possible unique and non-overlapping two-dimensional intervals of form: '(chrom1, start1, end1, chrom2, start2, end2)'. Each '(chrom1, start1, end1)' is created by taking a point 'C1' - '(chrom1, coord1)' and converting it to 'start1' and 'end1' such that 'start1 == coord1+E1[i]', 'end1 == coord1+E1[i+1]', where 'E1[i]' is one of the sorted 'expansion1' values. Overlaps between rectangles or expansion beyond the limits of chromosome are avoided.
'min.band.idx' and 'max.band.idx' parameters control whether a pair of 'C1' and 'C2' is skipped or not. If both of these parameters are not 'NULL' AND if both 'C1' and 'C2' share the same chromosome AND the delta of indices of 'C1' and 'C2' ('C1 index - C2 index') lays within '[min.band.idx, max.band.idx]' range - only then the pair will be used to create the intervals. Otherwise 'C1-C2' pair is filtered out. Note: if 'min.band.idx' and 'max.band.idx' are not 'NULL', i.e. band indices filtering is applied, then 'intervals2' parameter must be set to 'NULL'.
# \dontshow{
options(gmax.processes = 2)
# }
gdb.init_examples()
intervs1 <- gintervals(
c(1, 1, 2), c(100, 300, 200),
c(300, 500, 300)
)
intervs2 <- gintervals(
c(1, 2, 2), c(400, 1000, 3000),
c(800, 2000, 4000)
)
itr <- giterator.cartesian_grid(
intervs1, c(-20, 100), intervs2,
c(-40, -10, 50)
)
giterator.intervals(iterator = itr)
#> chrom1 start1 end1 chrom2 start2 end2
#> 1 chr1 180 300 chr1 560 590
#> 2 chr1 180 300 chr1 590 650
#> 3 chr1 380 500 chr1 560 590
#> 4 chr1 380 500 chr1 590 650
#> 5 chr1 180 300 chr2 1460 1490
#> 6 chr1 180 300 chr2 1490 1550
#> 7 chr1 180 300 chr2 3460 3490
#> 8 chr1 180 300 chr2 3490 3550
#> 9 chr1 380 500 chr2 1460 1490
#> 10 chr1 380 500 chr2 1490 1550
#> 11 chr1 380 500 chr2 3460 3490
#> 12 chr1 380 500 chr2 3490 3550
#> 13 chr2 230 350 chr1 560 590
#> 14 chr2 230 350 chr1 590 650
#> 15 chr2 230 350 chr2 1460 1490
#> 16 chr2 230 350 chr2 1490 1550
#> 17 chr2 230 350 chr2 3460 3490
#> 18 chr2 230 350 chr2 3490 3550
itr <- giterator.cartesian_grid(intervs1, c(-20, 50, 100))
giterator.intervals(iterator = itr)
#> chrom1 start1 end1 chrom2 start2 end2
#> 1 chr1 180 250 chr1 180 250
#> 2 chr1 180 250 chr1 250 300
#> 3 chr1 250 300 chr1 180 250
#> 4 chr1 250 300 chr1 250 300
#> 5 chr1 180 250 chr1 380 450
#> 6 chr1 180 250 chr1 450 500
#> 7 chr1 250 300 chr1 380 450
#> 8 chr1 250 300 chr1 450 500
#> 9 chr1 380 450 chr1 180 250
#> 10 chr1 380 450 chr1 250 300
#> 11 chr1 450 500 chr1 180 250
#> 12 chr1 450 500 chr1 250 300
#> 13 chr1 380 450 chr1 380 450
#> 14 chr1 380 450 chr1 450 500
#> 15 chr1 450 500 chr1 380 450
#> 16 chr1 450 500 chr1 450 500
#> 17 chr1 180 250 chr2 230 300
#> 18 chr1 180 250 chr2 300 350
#> 19 chr1 250 300 chr2 230 300
#> 20 chr1 250 300 chr2 300 350
#> 21 chr1 380 450 chr2 230 300
#> 22 chr1 380 450 chr2 300 350
#> 23 chr1 450 500 chr2 230 300
#> 24 chr1 450 500 chr2 300 350
#> 25 chr2 230 300 chr1 180 250
#> 26 chr2 230 300 chr1 250 300
#> 27 chr2 300 350 chr1 180 250
#> 28 chr2 300 350 chr1 250 300
#> 29 chr2 230 300 chr1 380 450
#> 30 chr2 230 300 chr1 450 500
#> 31 chr2 300 350 chr1 380 450
#> 32 chr2 300 350 chr1 450 500
#> 33 chr2 230 300 chr2 230 300
#> 34 chr2 230 300 chr2 300 350
#> 35 chr2 300 350 chr2 230 300
#> 36 chr2 300 350 chr2 300 350
itr <- giterator.cartesian_grid(intervs1, c(-20, 50, 100),
min.band.idx = -1,
max.band.idx = 0
)
giterator.intervals(iterator = itr)
#> chrom1 start1 end1 chrom2 start2 end2
#> 1 chr1 180 250 chr1 180 250
#> 2 chr1 180 250 chr1 250 300
#> 3 chr1 250 300 chr1 180 250
#> 4 chr1 250 300 chr1 250 300
#> 5 chr1 180 250 chr1 380 450
#> 6 chr1 180 250 chr1 450 500
#> 7 chr1 250 300 chr1 380 450
#> 8 chr1 250 300 chr1 450 500
#> 9 chr1 380 450 chr1 380 450
#> 10 chr1 380 450 chr1 450 500
#> 11 chr1 450 500 chr1 380 450
#> 12 chr1 450 500 chr1 450 500
#> 13 chr2 230 300 chr2 230 300
#> 14 chr2 230 300 chr2 300 350
#> 15 chr2 300 350 chr2 230 300
#> 16 chr2 300 350 chr2 300 350