add_hicpro_matrix_counts {HiCDCPlus} | R Documentation

## add_hicpro_matrix.counts

### Description

This function converts HiC-Pro matrix and bed outputs into a gi_list instance.

### Usage

    add_hicpro_matrix_counts(
      gi_list,
      absfile_path,
      matrixfile_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.
`absfile_path` | absfile BED out of HiC-Pro (e.g., 'rawdata_10000_abs.bed')
`matrixfile_path` | matrix count file out of HiC-Pro (e.g., 'rawdata_10000.matrix')
`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`.

[Package HiCDCPlus version 1.0.0 Index]