hicdc2hic {HiCDCPlus} | R Documentation

## 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')

[Package HiCDCPlus version 1.0.0 Index]