hic2icenorm_gi_list {HiCDCPlus} | R Documentation

## 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'))

[Package HiCDCPlus version 1.0.0 Index]