insulation_domainogram: Domainogram of insulation

In robinweide/GENOVA: GENOVA: expore the Hi-C

Domainogram of insulation

Description

Creates a domainogram of insulation scores for a genomic region of interest by calculating the insulation scores for a range of sliding square sizes.

Usage

insulation_domainogram(
  explist,
  chrom,
  start,
  end,
  window_range = c(5, 101),
  step = 2
)

Arguments

explist	Either a single GENOVA contacts object or list of GENOVA contacts objects.
chrom	One of the following: A character of length one indicating a chromosome name. A 3-column, 1-row data.frame in BED-format. A single character describing a locus in UCSC notation, e.g. "chr1:30,000,000-40,000,000". The latter two options automatically provide the start and end arguments too.
start, end	An integer of length 1 with a region's start and end position in basepairs.
window_range	An integer vector of length 2 noting the minimum and maximum size of the sliding square.
step	An integer of length 1 with the step size for incrementing the size of the sliding square.

Value

A domainogram_discovery object containing a data.frame with the insulation scores for the region of interest at various sizes of the sliding square.

Examples

## Not run: 
# Making a domainogram
domgram <- insulation_domainogram(list(WT = WT_20kb, KO = KO_20kb),
                                  chrom = "chr7", start = 25e6, end = 30e6)
                                 
# Plotting the domainogram
visualise(domgram)

## End(Not run)

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.