gdist: Calculates distribution of track expressions

In misha: Toolkit for Analysis of Genomic Data

Calculates distribution of track expressions

Description

Calculates distribution of track expressions' values over the given set of bins.

Usage

gdist(
  ...,
  intervals = NULL,
  include.lowest = FALSE,
  iterator = NULL,
  band = NULL
)

Arguments

...	pairs of 'expr', 'breaks' where 'expr' is a track expression and the breaks 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 expressions.
band	track expression band. If 'NULL' no band is used.

Details

This function calculates the distribution of values of the numeric track expressions over the given set of bins.

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]

'gdist' can work with any number of dimensions. If more than one 'expr'-'breaks' pair is passed, the result is a multidimensional vector, and an individual value can be accessed by [i1,i2,...,iN] notation, where 'i1' is the first track and 'iN' is the last track expression.

Value

N-dimensional vector where N is the number of 'expr'-'breaks' pairs.

See Also

gextract

Examples

gdb.init_examples()

## calculate the distribution of dense_track for bins:
## (0, 0.2], (0.2, 0.5] and (0.5, 1]
gdist("dense_track", c(0, 0.2, 0.5, 1))

## calculate two-dimensional distribution:
## dense_track vs. sparse_track
gdist("dense_track", seq(0, 1, by = 0.1), "sparse_track",
    seq(0, 2, by = 0.2),
    iterator = 100
)

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