Returns iterator intervals

Returns iterator intervals given track expression, scope, iterator and band.

giterator.intervals(
  expr = NULL,
  intervals = .misha$ALLGENOME,
  iterator = NULL,
  band = NULL,
  intervals.set.out = NULL
)

Arguments

expr

track expression

intervals

genomic scope

iterator

track expression iterator. If 'NULL' iterator is determined implicitly based on track expression.

band

track expression band. If 'NULL' no band is used.

intervals.set.out

intervals set name where the function result is optionally outputted

Value

If 'intervals.set.out' is 'NULL' a data frame representing iterator intervals.

Details

This function returns a set of intervals used by the iterator intervals for the given track expression, genomic scope, iterator and band. Some functions accept an iterator without accepting a track expression (like 'gtrack.create_pwm_energy'). These functions generate the values for each iterator interval by themselves. Use set 'expr' to 'NULL' to simulate the work of these functions.

If 'intervals.set.out' is not 'NULL' the result is saved as an intervals set. Use this parameter if the result size exceeds the limits of the physical memory.

See also

giterator.cartesian_grid

Examples

gdb.init_examples()

## iterator is set implicitly to bin size of 'dense' track
giterator.intervals("dense_track", gintervals(1, 0, 200))
#>   chrom start end
#> 1  chr1     0  50
#> 2  chr1    50 100
#> 3  chr1   100 150
#> 4  chr1   150 200

## iterator = 30
giterator.intervals("dense_track", gintervals(1, 0, 200), 30)
#>   chrom start end
#> 1  chr1     0  30
#> 2  chr1    30  60
#> 3  chr1    60  90
#> 4  chr1    90 120
#> 5  chr1   120 150
#> 6  chr1   150 180
#> 7  chr1   180 200

## iterator is an intervals set named 'annotations'
giterator.intervals("dense_track", .misha$ALLGENOME, "annotations")
#>   chrom start   end
#> 1  chr1    20  2000
#> 2  chr1  2500  2600
#> 3  chr2    20  2000
#> 4  chr2  3000  8000
#> 5  chr2  9000 11000
#> 6  chr2 12000 12001
#> 7  chr2 13000 14000
#> 8  chr2 15000 15500

## iterator is set implicitly to intervals of 'array_track' track
giterator.intervals("array_track", gintervals(1, 0, 200))
#>   chrom start end
#> 1  chr1     0  50
#> 2  chr1   100 150

## iterator is a rectangle 100000 by 50000
giterator.intervals(
    "rects_track",
    gintervals.2d(chroms1 = 1, chroms2 = "chrX"),
    c(100000, 50000)
)
#>    chrom1 start1  end1 chrom2 start2   end2
#> 1    chr1  0e+00 1e+05   chrX      0  50000
#> 2    chr1  1e+05 2e+05   chrX      0  50000
#> 3    chr1  2e+05 3e+05   chrX      0  50000
#> 4    chr1  3e+05 4e+05   chrX      0  50000
#> 5    chr1  4e+05 5e+05   chrX      0  50000
#> 6    chr1  0e+00 1e+05   chrX  50000 100000
#> 7    chr1  1e+05 2e+05   chrX  50000 100000
#> 8    chr1  2e+05 3e+05   chrX  50000 100000
#> 9    chr1  3e+05 4e+05   chrX  50000 100000
#> 10   chr1  4e+05 5e+05   chrX  50000 100000
#> 11   chr1  0e+00 1e+05   chrX 100000 150000
#> 12   chr1  1e+05 2e+05   chrX 100000 150000
#> 13   chr1  2e+05 3e+05   chrX 100000 150000
#> 14   chr1  3e+05 4e+05   chrX 100000 150000
#> 15   chr1  4e+05 5e+05   chrX 100000 150000
#> 16   chr1  0e+00 1e+05   chrX 150000 200000
#> 17   chr1  1e+05 2e+05   chrX 150000 200000
#> 18   chr1  2e+05 3e+05   chrX 150000 200000
#> 19   chr1  3e+05 4e+05   chrX 150000 200000
#> 20   chr1  4e+05 5e+05   chrX 150000 200000