gpartition: Partitions the values of track expression

Description

Converts the values of track expression to intervals that match corresponding bin.

Usage

gpartition(
  expr = NULL,
  breaks = NULL,
  intervals = NULL,
  include.lowest = FALSE,
  iterator = NULL,
  band = NULL,
  intervals.set.out = NULL
)

Value

If 'intervals.set.out' is 'NULL' a set of intervals with an additional column that indicates the corresponding bin index.

Arguments

expr: track expression
breaks: breaks that determine the bin
intervals: genomic scope for which the function is applied
include.lowest: if 'TRUE', the lowest value of the range determined by breaks is included
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 converts first the values of track expression into 1-based bin's index according 'breaks' argument. It returns then the intervals with the corresponding bin's index.

The range of bins is determined by 'breaks' argument. For example: 'breaks=c(x1, x2, x3, x4)' represents three different intervals (bins): (x1, x2], (x2, x3], (x3, x4].

If 'include.lowest' is 'TRUE' the the lowest value will be included in the first interval, i.e. in [x1, x2].

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.

Examples

Run this code

# \dontshow{
options(gmax.processes = 2)
# }

gdb.init_examples()
breaks <- seq(0, 0.2, by = 0.05)
gpartition("dense_track", breaks, gintervals(1, 0, 5000))