giterator.intervals: Returns iterator intervals

In misha: Toolkit for Analysis of Genomic Data

Returns iterator intervals

Description

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

Usage

giterator.intervals(
  expr = NULL,
  intervals = .misha$ALLGENOME,
  iterator = NULL,
  band = NULL,
  intervals.set.out = NULL,
  interval_relative = FALSE,
  partial_bins = c("clip", "exact", "drop")
)

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
interval_relative	if TRUE, and iterator is numeric, bins start at each interval's start position instead of chromosome position 0. Returns intervalID column. Default: FALSE.
partial_bins	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).

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.

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.

Value

If 'intervals.set.out' is 'NULL' a data frame representing iterator intervals. When 'interval_relative' is TRUE, includes an 'intervalID' column.

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))

## iterator = 30
giterator.intervals("dense_track", gintervals(1, 0, 200), 30)

## iterator is an intervals set named 'annotations'
giterator.intervals("dense_track", .misha$ALLGENOME, "annotations")

## iterator is set implicitly to intervals of 'array_track' track
giterator.intervals("array_track", gintervals(1, 0, 200))

## iterator is a rectangle 100000 by 50000
giterator.intervals(
    "rects_track",
    gintervals.2d(chroms1 = 1, chroms2 = "chrX"),
    c(100000, 50000)
)

## 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)

misha documentation built on Jan. 28, 2026, 1:07 a.m.