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

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Documentation for package ‘HiCBricks’ version 1.23.0

• 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_data_from_sparse	Identify compartments in the Hi-C data
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