hicdc2hic: hicdc2hic

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

hicdc2hic

Description

This function converts various modes from HiCDCPlus gi_list (uniformly binned) instance back into a .hic file with the mode passed as counts that can be retrieved using Juicer Dump (https://github.com/aidenlab/juicer/wiki/Data-Extraction) with 'NONE' normalization.

Usage

hicdc2hic(
  gi_list,
  hicfile,
  mode = "normcounts",
  chrs = NULL,
  gen_ver = "hg19",
  memory = 8
)

Arguments

gi_list	List of GenomicInteractions objects where each object named with chromosomes contains intra-chromosomal interaction information (minimally containing counts and genomic distance in mcols(gi_list)— see ?gi_list_validate for a detailed explanation of valid gi_list instances).
hicfile	the path to the .hic file
mode	What to put to the .hic file as score. Allowable options are: 'pvalue' for -log10 significance p-value, 'qvalue' for -log10 FDR corrected p-value, 'normcounts' for raw counts/expected counts, and 'zvalue' for standardized counts (raw counts-expected counts)/modeled standard deviation of expected counts and 'raw' to pass-through 'raw counts. Defaults to 'normcounts'.
chrs	select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to chromosomes in gi_list.
gen_ver	genomic assembly version: e.g., default 'hg19'
memory	Java memory to generate .hic files. Defaults to 8. Up to 64 is recommended for higher resolutions.

Value

path of the .hic file.

Examples

outdir<-paste0(tempdir(check=TRUE),'/')
gi_list<-generate_binned_gi_list(50e3,chrs='chr22')
gi_list<-add_hic_counts(gi_list,
hic_path=system.file("extdata", "GSE63525_HMEC_combined_example.hic",
package = "HiCDCPlus"))
hicdc2hic(gi_list,hicfile=paste0(outdir,'out.hic'),
mode='raw')

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