hic2icenorm_gi_list: hic2icenorm_gi_list

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

hic2icenorm_gi_list

Description

This function converts a .hic file into a gi_list instance with ICE normalized counts on the counts column for TAD annotation using a copy of TopDom (see ?TopDom_0.0.2) as well as an (optional) .hic file with ICE normalized counts for visualization with Juicebox. This function requires installing the Bioconductor package HiTC.

Usage

hic2icenorm_gi_list(
  hic_path,
  binsize = 50000,
  chrs = NULL,
  hic_output = FALSE,
  gen = "Hsapiens",
  gen_ver = "hg19",
  Dthreshold = Inf
)

Arguments

hic_path	Path to the .hic file.
binsize	Desired bin size in bp (default 50000).
chrs	select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to chromosomes in gen and gen_ver except 'chrY' and 'chrM'.
hic_output	If TRUE, a .hic file with the name gsub("\.hic$","_icenorm.hic",hic_path) is generated containing the ICE normalized counts under 'NONE' normalization.
gen	name of the species: e.g., default 'Hsapiens'
gen_ver	genomic assembly version: e.g., default 'hg19'
Dthreshold	maximum distance (included) to check for significant interactions, defaults to maximum in the data.

Value

a thresholded gi_list instance with ICE normalized intra-chromosomal counts for further use with this package, HiCDCPlus.

Examples

hic_path<-system.file("extdata", "GSE63525_HMEC_combined_example.hic",
package = "HiCDCPlus")
gi_list=hic2icenorm_gi_list(hic_path,binsize=50e3,chrs=c('chr22'))

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