dominating_signal.HiCcomparator: Calculates coverage or decay of Hi-C maps.

In rz6/CopulaHiC: Hi-C differential analysis via dependency modelling of chromatin interactions with generalized linear models

Description

Computes coverages or decays of every Hi-C maps in both data sets of given HiCcomparator object. Coverage is defined as sum of contacts on given bin. Decay is sum or mean of contacts for every diagonal.

Usage

## S3 method for class 'HiCcomparator'
dominating_signal(hic.comparator, which.signal = c("coverage", "decay")[1])

Arguments

hic.comparator	object of type HiCcomparator
which.signal	character either coverage or decay, which signal to calculate

Value

dataframe with following columns: (i, sum.contacts, mean.contacts, sd.contacts, name, dataset), which can be used to conveniently visualise coverages or decays (see examples)

See Also

HiCcomparator on how to construct HiCcomparator object

Examples

# first create HiCcomparator object - see ?HiCcomparator for examples
coverage <- dominating_signal(hic.comparator)
# visualise results
library("ggplot2")
ggplot(coverage, aes(x = i, y = sum.contacts, color = dataset)) +
geom_point(size = 0.5) +
 geom_smooth(alpha = 0.5) +
 facet_wrap(~ name, ncol = 1, scales = "free") +
 theme(legend.position = "bottom")
# get decay
decay <- dominating_signal(hic.comparator, which.signal = "decay")
ggplot(decay[decay$diagonal != 0,], aes(x = diagonal, y = mean.contacts, color = dataset)) +
geom_point(size = 0.5) +
 scale_x_log10() +
 scale_y_log10() +
 facet_wrap(~ name, ncol = 1, scales = "free") +
 theme(legend.position = "bottom")

rz6/CopulaHiC documentation built on Dec. 31, 2019, 9:19 a.m.