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,
interval_relative = FALSE,
partial_bins = c("clip", "exact", "drop")
)track expression
genomic scope
track expression iterator. If 'NULL' iterator is determined implicitly based on track expression.
track expression band. If 'NULL' no band is used.
intervals set name where the function result is optionally outputted
if TRUE, and iterator is numeric, bins start at each interval's start position instead of chromosome position 0. Returns intervalID column. Default: FALSE.
how to handle partial bins at interval boundaries when interval_relative is TRUE. One of "clip" (default, truncate last bin to interval boundary), "exact" or "drop" (only output full-size bins).
If 'intervals.set.out' is 'NULL' a data frame representing iterator intervals. When 'interval_relative' is TRUE, includes an 'intervalID' column.
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.
When 'interval_relative' is TRUE, bins are aligned to each input interval's start position rather than chromosome position 0. This mode requires a numeric iterator (binsize) and returns an additional 'intervalID' column indicating which input interval spawned each bin.
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
## interval_relative mode: bins aligned to each interval's start
intervs <- gintervals(1, c(100, 500), c(300, 700))
giterator.intervals(NULL, intervs, iterator = 50, interval_relative = TRUE)
#> chrom start end intervalID
#> 1 chr1 100 150 1
#> 2 chr1 150 200 1
#> 3 chr1 200 250 1
#> 4 chr1 250 300 1
#> 5 chr1 500 550 2
#> 6 chr1 550 600 2
#> 7 chr1 600 650 2
#> 8 chr1 650 700 2