gpartition: Partitions the values of track expression

In misha: Toolkit for Analysis of Genomic Data

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
)

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.

Value

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

See Also

gscreen, gextract, glookup, gdist

Examples

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

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