Defines modification rules for a one-dimensional iterator in a virtual track

Defines modification rules for a one-dimensional iterator in a virtual track.

gvtrack.iterator(vtrack = NULL, dim = NULL, sshift = 0, eshift = 0)

Arguments

vtrack

virtual track name

dim

use 'NULL' or '0' for 1D iterators. '1' converts 2D iterator to (chrom1, start1, end1) , '2' converts 2D iterator to (chrom2, start2, end2)

sshift

shift of 'start' coordinate

eshift

shift of 'end' coordinate

Value

None.

Details

This function defines modification rules for one-dimensional iterator intervals in a virtual track.

'dim' converts a 2D iterator interval (chrom1, start1, end1, chrom2, start2, end2) to a 1D interval. If 'dim' is '1' the interval is converted to (chrom1, start1, end1). If 'dim' is '2' the interval is converted to (chrom2, start2, end2). If 1D iterator is used 'dim' must be set to 'NULL' or '0' (meaning: no conversion is made).

Iterator interval's 'start' coordinate is modified by adding 'sshift'. Similarly 'end' coordinate is altered by adding 'eshift'.

A shifted interval that runs past a chromosome boundary is clamped to it. If nothing is left of it - it falls entirely outside the chromosome, or the shifts collapse it to zero length - the virtual track returns 'NaN'.

See also

gvtrack.create, gvtrack.iterator.2d

Examples

gdb.init_examples()

gvtrack.create("vtrack1", "dense_track")
gvtrack.iterator("vtrack1", sshift = 200, eshift = 200)
gextract("dense_track", "vtrack1", gintervals(1, 0, 500))
#>    chrom start end dense_track vtrack1 intervalID
#> 1   chr1     0  50   0.1777778    0.16          1
#> 2   chr1    50 100   0.1600000    0.20          1
#> 3   chr1   100 150   0.1800000    0.16          1
#> 4   chr1   150 200   0.1600000    0.16          1
#> 5   chr1   200 250   0.1600000    0.16          1
#> 6   chr1   250 300   0.2000000    0.06          1
#> 7   chr1   300 350   0.1600000    0.06          1
#> 8   chr1   350 400   0.1600000    0.02          1
#> 9   chr1   400 450   0.1600000    0.04          1
#> 10  chr1   450 500   0.0600000    0.00          1

gvtrack.create("vtrack2", "dense_track")
gvtrack.iterator("vtrack2", dim = 1)
gextract("vtrack2", gintervals.2d(1, 0, 1000, 1, 0, -1),
    iterator = "rects_track"
)
#> NULL