# Framework for Storing and Accessing Hi-C Data Through HDF Files

## Documentation for package ‘HiCBricks’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BrickContainer_change_experiment_name | Change the location of HDF files in the BrickContainer object
BrickContainer_change_output_directory | Change the location of HDF files in the BrickContainer object
BrickContainer_get_path_to_file | Get the path to HDF files present in the Brick container.
BrickContainer_list_chromosomes | Return the descriptive name of the BrickContainer
BrickContainer_list_experiment_name | Return the descriptive name of the BrickContainer
BrickContainer_list_files | Get the list of HDF files present in the Brick container.
BrickContainer_list_output_directory | Return the output directory of the BrickContainer
BrickContainer_list_resolutions | Return the descriptive name of the BrickContainer
BrickContainer_unlink_resolution | Remove links to all Hi-C matrices for a given resolution.
Brick_add_ranges | Store a ranges object in the Brick store.
Brick_call_compartments | Identify compartments in the Hi-C data
Brick_export_to_sparse | Export an entire resolution from a given BrickContainer as a upper triangle sparse matrix
Brick_fetch_range_index | Returns the position of the supplied ranges in the binning table associated to the Hi-C experiment.
Brick_fetch_row_vector | Return row or col vectors.
Brick_get_bintable | Returns the binning table associated to the Hi-C experiment.
Brick_get_chrominfo | Get the chrominfo for the Hi-C experiment.
Brick_get_entire_matrix | Return an entire matrix for provided chromosome pair for a resolution.
Brick_get_matrix | Return a matrix subset.
Brick_get_matrix_mcols | Get the matrix metadata columns in the Brick store.
Brick_get_matrix_within_coords | Return a matrix subset between two regions.
Brick_get_ranges | Fetch the ranges associated to a rangekey or chromosome.
Brick_get_values_by_distance | Return values separated by a certain distance.
Brick_get_vector_values | Return a N dimensional vector selection.
Brick_list_matrices | List the matrix pairs present in the Brick store.
Brick_list_matrix_mcols | List the matrix metadata columns in the Brick store.
Brick_list_mcool_normalisations | Get all available normalisations in an mcool file.
Brick_list_mcool_resolutions | Get all available normalisations in an mcool file.
Brick_list_rangekeys | List the ranges tables stored within the Brick.
Brick_list_ranges_mcols | Find out what metadata columns are associated to a ranges with a certain name
Brick_load_cis_matrix_till_distance | Load a NxN dimensional sub-distance _cis_ matrix into the Brick store.
Brick_load_data_from_mcool | Load a NxN dimensional matrix into the Brick store from an mcool file.
Brick_load_matrix | Load a NxM dimensional matrix into the Brick store.
Brick_local_score_differentiator | Do TAD Calls with Local Score Differentiator on a Hi-C matrix
Brick_make_ranges | Creates a ranges object from provided vectors.
Brick_matrix_dimensions | Return the dimensions of a matrix
Brick_matrix_exists | Check if a chromosome pair exists.
Brick_matrix_filename | Return the filename of the loaded matrix
Brick_matrix_isdone | Check if a matrix has been loaded for a chromosome pair.
Brick_matrix_issparse | Check if a matrix for a chromosome pair is sparse.
Brick_matrix_maxdist | Get the maximum loaded distance from the diagonal of any matrix.
Brick_matrix_minmax | Return the value range of the matrix
Brick_mcool_normalisation_exists | Check if a normalisation exists in an mcool file.
Brick_rangekey_exists | Check to see if the Brick contains a ranges with a certain name.
Brick_return_region_position | Provides the overlapping position (within) from the bintable.
Brick_vizart_plot_heatmap | Create the entire HDF5 structure and load the bintable
Create_many_Bricks | Create the entire HDF5 structure and load the bintable
Create_many_Bricks_from_mcool | Create the entire HDF5 structure and load the bintable from a mcool file
HiCBricks | A package for storing, accessing and plotting Hi-C data
load_BrickContainer | Create a BrickContainer object from a JSON file