Brick_get_matrix_within_coords {HiCBricks} | R Documentation |
Brick_get_matrix_within_coords
will fetch a matrix subset after
creating an overlap operation between both regions and the bintable
associated to the Brick store.
This function calls Brick_get_matrix
.
Brick_get_matrix_within_coords(Brick, x.coords, y.coords, force = FALSE, FUN = NULL)
Brick |
Required. A string specifying the path to the Brick store created with CreateBrick. |
x.coords |
Required. A string specifying the region to subset on the rows. It takes the form chr:start:end. An overlap operation with the associated bintable will be done to identify the bins to subset on the row |
y.coords |
Required. A string specifying the region to subset on the rows. It takes the form chr:start:end. An overlap operation with the associated bintable will be done to identify the bins to subset on the column |
force |
Optional. Default FALSE If true, will force the retrieval operation when matrix contains loaded data until a certain distance. |
FUN |
Optional. If provided a data transformation with FUN will be applied before the matrix is returned. |
Returns a matrix of dimension x.coords binned length by y.coords binned length. This may differ based on FUN.
Brick_get_matrix
to get matrix by using matrix
coordinates, Brick_get_values_by_distance
to get values
separated at a certain distance, Brick_fetch_row_vector
to get values in a certain row/col and subset them,
Brick_get_vector_values
to get values using matrix
coordinates.
Brick.file <- system.file("extdata", "test.hdf", package = "HiCBricks") Brick_get_matrix_within_coords(Brick = Brick.file, x.coords = "chr19:40000:2000000", y.coords = "chr19:40000:2000000") Brick_get_matrix_within_coords(Brick = Brick.file, x.coords = "chr19:40000:2000000", y.coords = "chr19:40000:2000000", FUN = mean) Brick_get_matrix_within_coords(Brick = Brick.file, x.coords = "chr19:40000:2000000", y.coords = "chr19:40000:2000000", FUN = median)