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


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Documentation for package ‘HiCBricks’ version 1.2.0

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Brick_add_ranges Store a ranges object in the Brick store.
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_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
CreateBrick Create the entire HDF5 structure and load the bintable
CreateBrick_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