RCP: Relative Contact Probabilities

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

Relative Contact Probabilities

Description

Produce a dataframe with the probabilities of contacts in a set of distance-bins. Bins are created on a log scale, which leads to equal amounts of datapoints per bin.

Usage

RCP(
  explist,
  bedlist = NULL,
  chromsToUse = NULL,
  maxDistance = NULL,
  genomeWide = NULL
)

Arguments

explist	List of GENOVA contacts-objects from 'load_contacts()'.
bedlist	A named list of BED-like dataframes of the regions of interest.
chromsToUse	A vector containing the chromosome-names of interest.
maxDistance	The maximal distance to calculate RCPs for.
genomeWide	Normalise with genome-wide counts or per-chromosome (default).

Value

An RCP_discovery object containing:

raw	a per-distance probability
smooth	a log10-mean smoothed probability

Resolution recommendation

40kb-500kb

Author(s)

Robin H. van der Weide, [e-mail]

Examples

# Calculate the RCP of chromosome 1
## Not run: 
RCP_out = RCP(experimentList = list('WT' = WT_1MB), chromsToUse = 'chr1')

# Plot the RCP
visualise(RCP_out)

## End(Not run)

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