giterator.cartesian_grid: Creates a cartesian-grid iterator

In misha: Toolkit for Analysis of Genomic Data

Creates a cartesian-grid iterator

Description

Creates a cartesian grid two-dimensional iterator that can be used by any function that accepts an iterator argument.

Usage

giterator.cartesian_grid(
  intervals1 = NULL,
  expansion1 = NULL,
  intervals2 = NULL,
  expansion2 = NULL,
  min.band.idx = NULL,
  max.band.idx = NULL
)

Arguments

intervals1	one-dimensional intervals
expansion1	an array of integers that define expansion around intervals1 centers
intervals2	one-dimensional intervals. If 'NULL' then 'intervals2' is considered to be equal to 'intervals1'
expansion2	an array of integers that define expansion around intervals2 centers. If 'NULL' then 'expansion2' is considered to be equal to 'expansion1'
min.band.idx, max.band.idx	integers that limit iterator intervals to band

Details

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'.

Value

A list containing the definition of cartesian iterator.

See Also

giterator.intervals

Examples

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)

itr <- giterator.cartesian_grid(intervs1, c(-20, 50, 100))
giterator.intervals(iterator = itr)

itr <- giterator.cartesian_grid(intervs1, c(-20, 50, 100),
    min.band.idx = -1,
    max.band.idx = 0
)
giterator.intervals(iterator = itr)

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