gvtrack.iterator {misha} | R Documentation |
Defines modification rules for a one-dimensional iterator in a virtual track
Description
Defines modification rules for a one-dimensional iterator in a virtual track.
Usage
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 |
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'.
Value
None.
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))
gvtrack.create("vtrack2", "dense_track")
gvtrack.iterator("vtrack2", dim = 1)
gextract("vtrack2", gintervals.2d(1, 0, 1000, 1, 0, -1),
iterator = "rects_track"
)