add_hic_counts {HiCDCPlus} | R Documentation

## add_hic_counts

### Description

This function adds counts from a .hic file into a valid, binned, gi_list instance.

### Usage

    add_hic_counts(gi_list, hic_path, chrs = NULL, add_inter = FALSE)

### Arguments

`gi_list` | valid, uniformly binned gi_list instance. See `?gi_list_validate` and `gi_list_binsize_detect` for details.
`hic_path` | path to the .hic file
`chrs` | a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes in the `gi_list` instance.
`add_inter` | Interchromosomal interaction counts added as a 1D feature named 'inter' on regions metadata handle of each gi_list element (e.g., `gi_list[[1]]@regions@elementMetadata` or not; default FALSE

### Value

`gi_list` instance with counts on the metadata (e.g., `mcols(gi_list[[1]])` handle on each list element, and 'inter' on regions metadata handle of each element if `add_inter=TRUE`.

### Examples

    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"))

[Package HiCDCPlus version 1.0.0 Index]