Ps: Compute the law of distance-dependent contact frequency,...

In js2264/cooleR: Analysing cool files in R with HiContacts

Compute the law of distance-dependent contact frequency, a.k.a. P(s)

Description

P(s) will be approximated if no pairs are provided, or the exact P(s) will be computed if a .pairs file is added to the HiCExperiment object using pairsFile(x) <- "...".

Usage

distanceLaw(x, coords, ...)

## S4 method for signature 'GInteractions,missing'
distanceLaw(x, by_chr = FALSE)

## S4 method for signature 'HiCExperiment,missing'
distanceLaw(
  x,
  by_chr = FALSE,
  filtered_chr = c("XII", "chrXII", "chr12", "12", "Mito", "MT", "chrM")
)

## S4 method for signature 'PairsFile,missing'
distanceLaw(
  x,
  by_chr = FALSE,
  filtered_chr = c("XII", "chrXII", "chr12", "12", "Mito", "MT", "chrM"),
  chunk_size = 1e+05
)

## S4 method for signature 'HiCExperiment,GRanges'
distanceLaw(x, coords, chunk_size = 1e+05)

## S4 method for signature 'PairsFile,GRanges'
distanceLaw(x, coords, chunk_size = 1e+05)

localDistanceLaw(x, coords = coords)

Arguments

x	A HiCExperiment object
coords	GRanges to specify which genomic loci to use when computing P(s)
...	Arguments passed to corresponding method
by_chr	by_chr
filtered_chr	filtered_chr
chunk_size	For pairs files which do not fit in memory, pick a number of pairs to parse by chunks (1e7 should be a good compromise)

Value

a tibble

Examples

contacts_yeast <- contacts_yeast()
ps <- distanceLaw(contacts_yeast)
ps
local_ps <- localDistanceLaw(
    contacts_yeast,
    GenomicRanges::GRanges(
        c("telomere" = "II:1-20000", "arm" = "II:300001-700000")
    )
)
local_ps

js2264/cooleR documentation built on Jan. 29, 2024, 10:47 p.m.