call_TAD_insulation: Call TADs from insulation scores

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

Call TADs from insulation scores

Description

Runs peak detection on the genome wide insulation scores to identify insulation valleys that correspond well to TAD boundaries.

Usage

call_TAD_insulation(IS_discovery, method = "crane", min_strength = 0.1)

Arguments

IS_discovery	A GENOVA IS_discovery object as created by insulation_score().
method	A character vector of length 1. Currently, only "crane" is implemented.
min_strength	A numeric vector of length 1 setting a threshold on the boundary strength wherein higher means stronger boundaries.

Details

The Crane et al. (2015) method calculates a delta vector across the insulation score defined by the difference between 100kb to the right and left of a central bin. This delta crosses zero at local extrema, of which the minima are kept. Subsequently, potential boundaries are filtered on the boundary strength defined as the difference in the delta vector between the nearest 5' local maximum and 3' local minimum relative to the boundaray.

Value

A list containing BED-formatted data.frames for each experiment in the IS_discovery object.

See Also

insulation_score for calculating insulation scores.

Examples

## Not run: 
# Calculating insulation scores
ins <- insulation_score(list(WT_20kb, KO_20kb), window = 25)

# Calling TADs from the insulation score
tadlist <- call_TAD_insulation(ins)

# Plotting TADs
hic.matrixplot(
  exp1 = WT_20kb,
  chrom = "chr7",
  start = 25e6,
  end = 30e6,
  tads = tadlist$WT_20kb
)

## End(Not run)

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