Brick_get_matrix {HiCBricks} | R Documentation |
Brick_get_matrix
will fetch a matrix subset between row values
ranging from min(x.vector) to max(x.vector) and column values ranging from
min(x.vector) to max(x.vector)
Brick_get_matrix(Brick, chr1, chr2, x.vector, y.vector, force = FALSE, FUN = NULL)
Brick |
Required. A string specifying the path to the Brick store created with CreateBrick. |
chr1 |
Required. A character vector of length 1 specifying the chromosome corresponding to the rows of the matrix |
chr2 |
Required. A character vector of length 1 specifying the chromosome corresponding to the columns of the matrix |
x.vector |
Required. A one-dimensional numeric vector specifying the rows to subset. |
y.vector |
Required. A one-dimensional numeric vector specifying the columns to subset. |
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.vector length by y.vector length. This may differ based on the operations with FUN.
Brick_get_matrix_within_coords
to get matrix by using
matrix genomic coordinates, Brick_get_values_by_distance
to
get values separated at a certain distance,
Brick_fetch_row_vector
to getvalues 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(Brick = Brick.file, chr1 = "chr19", chr2 = "chr19", x.vector = c(1:10), y.vector = c(1:10))