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
)

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

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.

Value

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

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)
)

misha documentation built on Sept. 14, 2023, 5:08 p.m.