generate_binned_gi_list: generate_binned_gi_list

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

generate_binned_gi_list

Description

Generates a valid uniformly binned gi_list instance.

Usage

generate_binned_gi_list(
  binsize,
  chrs = NULL,
  Dthreshold = 2e+06,
  gen = "Hsapiens",
  gen_ver = "hg19"
)

Arguments

binsize	Desired binsize in bp, e.g., 5000, 25000.
chrs	a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes except "Y", and "M" for the specified gen and gen_ver.
Dthreshold	maximum distance (included) to check for significant interactions, defaults to 2e6 or maximum in the data; whichever is smaller.
gen	name of the species: e.g., default 'Hsapiens'.
gen_ver	genomic assembly version: e.g., default 'hg19'.

Value

a valid, uniformly binned gi_list instance.

Examples

gi_list<-generate_binned_gi_list(1e6,chrs='chr22')

mervesa/HiCDCPlus documentation built on June 8, 2022, 3:43 a.m.