HiCBricks: A package for storing, accessing and plotting Hi-C data
In koustav-pal/HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files

HiCBricks

R Documentation

A package for storing, accessing and plotting Hi-C data

Description

HiCBricks is a package allowing users to flexibly import and work with Hi-C data

Details

Using HiCBricks users are able to import Hi-C matrices stored in various formats into an HDF structure. This is the Brick file. You can then access the Hi-C data using accessor functions. Since the data is stored in an HDF file, if you have the Brick (HDF) file, you can keep on accessing the same file an infinite number of times.

Users can also associate different ranges objects with the HDF file.

The HDF file must have the same structure as followed by HiCBricks

Users can then move forward and create analysis pipelines and statistical methods based on HiCBricks HDF files without worrying about the underlying data structure. To showcase this, Local score differentiator (LSD) our novel TAD calling procedure comes packaged with HiCBricks.

You are also able to plot Hi-C data using HiCBricks functions. There are a few types. You can create,

a square heatmap
a rotated heatmap
two group square/rotated heatmaps
both heatmaps until a certain distance
plot TADs on both heatmaps

Brick creation

Create_many_Bricks - Create the HDF data structures. We refer to the HDF files as Bricks
Create_many_Bricks_from_mcool - Create the complete Brick data structure from an mcool file.

Matrix loaders

Brick_load_matrix - Load a complete nxm dimensional matrix.
Brick_load_cis_matrix_till_distance - Load a sam chromosome nxn dimensional matrix until a certain distance.
Brick_load_data_from_mcool - Load parts of the data from the 4DN consortium generated mcool files.

Matrix Accessors

Brick_get_matrix_within_coords - Fetches a matrix within the provided genomic coordinates.
Brick_get_matrix - Fetches a matrix within the provided x and y coordinates.
Brick_get_values_by_distance - Fetch all values corresponding to interactions between genomic loci separated by the corresponding value.
Brick_fetch_row_vector - Fetch all values at a given row or column.

All of the functions above can be subsetted and contain further value transformations.

Ranges operators

Brick_get_bintable - All HiCBricks Brick files contain a binning table containing the coordinate information of the matrix. This fetches the associated binning table.
Brick_add_ranges - Add a ranges object to the Brick file.
Brick_get_ranges - Get a ranges object associated to a Brick file.
Brick_fetch_range_index - Provided a set of coordinate vectors, get the corresponding rows/cols overlapping with those coordinates.
Brick_make_ranges - Create a granges object from provided vectors.
Brick_return_region_position - Get the row/col number corresponding to coordinates spelled out in human readable format.

Other functions

Brick_local_score_differentiator - Use the LSD TAD calling procedure to do some TAD calls.
Brick_vizart_plot_heatmap - Plot pretty heatmaps.

Utility functions

Brick_get_chrominfo - Get the basic information regarding the Brick file. Which chromosomes are present, dimension of the matrix and the total length of the chromosome.
Brick_get_matrix_mcols - Get the matrix metadata information. Such as, row sums, coverage information and how sparse regions near the diagonal are.
Brick_list_matrices - List all the matrices present in the Brick file. Alongside, also provide information such as if the matrix has been loaded or not, min max values, e.t.c
Brick_list_rangekeys - List the names of the ranges present in the Brick file.
Brick_rangekey_exists - Answers the question, is this rangekey present in the Brick file?
Brick_list_ranges_mcols - List the names of metadata columns associated to a ranges object in the Brick file.
Brick_matrix_dimensions - Get the dimensions of a given matrix.
Brick_matrix_exists - Answers the question, has a matrix been created for this Brick store?
Brick_matrix_filename - Answers the question, what is the name of the file used to load this particular matrix?
Brick_matrix_isdone - Answers the question, has this matrix been loaded already?
Brick_matrix_issparse - Answers the question, was this matrix defined as a sparse matrix while loading?
Brick_matrix_maxdist - If Brick_load_cis_matrix_till_distance was used for loading data, then this function will tell you until what distance data was loaded.
Brick_matrix_minmax - Outputs the value range of the matrix.

mcool utility functions

Brick_list_mcool_normalisations - List the names of normalisation vectors that can be present in a mcool file.
Brick_mcool_normalisation_exists - Check if a specific normalisation vector exists in an mcool file.
Brick_list_mcool_resolutions - List the resolutions present in an mcool file.