misha (version 4.2.9)

gcis_decay: Calculates distribution of contact distances

Description

Calculates distribution of contact distances.

Usage

gcis_decay(
  expr = NULL,
  breaks = NULL,
  src = NULL,
  domain = NULL,
  intervals = NULL,
  include.lowest = FALSE,
  iterator = NULL,
  band = NULL
)

Value

2-dimensional vector representing the distribution of contact distances for inter and intra domains.

Arguments

expr

track expression

breaks

breaks that determine the bin

src

source intervals

domain

domain intervals

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

2D track expression iterator. If 'NULL' iterator is determined implicitly based on track expressions.

band

track expression band. If 'NULL' no band is used.

Details

A 2D iterator interval '(chrom1, start1, end1, chrom2, start2, end2)' is said to represent a contact between two 1D intervals I1 and I2: '(chrom1, start1, end1)' and '(chrom2, start2, end2)'.

For contacts where 'chrom1' equals to 'chrom2' and I1 is within source intervals the function calculates the distribution of distances between I1 and I2. The distribution is calculated separately for intra-domain and inter-domain contacts.

An interval is within source intervals if the unification of all source intervals fully overlaps it. 'src' intervals are allowed to contain overlapping intervals.

Two intervals I1 and I2 are within the same domain (intra-domain contact) if among the domain intervals exists an interval that fully overlaps both I1 and I2. Otherwise the contact is considered to be inter-domain. 'domain' must contain only non-overlapping intervals.

The distance between I1 and I2 is the absolute distance between the centers of these intervals, i.e.: '|(start1 + end1 - start2 - end2) / 2|'.

The range of distances for which the distribution is calculated is defined 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]

See Also

gdist, gtrack.2d.import_contacts

Examples

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

gdb.init_examples()

src <- rbind(
    gintervals(1, 10, 100),
    gintervals(1, 200, 300),
    gintervals(1, 400, 500),
    gintervals(1, 600, 700),
    gintervals(1, 7000, 9100),
    gintervals(1, 9000, 18000),
    gintervals(1, 30000, 31000),
    gintervals(2, 1130, 15000)
)

domain <- rbind(
    gintervals(1, 0, 483000),
    gintervals(2, 0, 300000)
)

gcis_decay("rects_track", 50000 * (1:10), src, domain)