Convert between BPCells matrix and R objects.

BPCells matrices can be interconverted with Matrix package dgCMatrix sparse matrices, as well as base R dense matrices (though this may result in high memory usage for large matrices)

Usage

# Convert to R from BPCells
as(bpcells_mat, "dgCMatrix") # Sparse matrix conversion
as.matrix(bpcells_mat) # Dense matrix conversion

# Convert to BPCells from R
as(dgc_mat, "IterableMatrix")

Examples

mat <- get_demo_mat()[1:2, 1:2]
mat
#> 2 x 2 IterableMatrix object with class MatrixSubset
#> 
#> Row names: ENSG00000272602, ENSG00000250312
#> Col names: TTTAGCAAGGTAGCTT-1, AGCCGGTTCCGGAACC-1
#> 
#> Data type: uint32_t
#> Storage order: column major
#> 
#> Queued Operations:
#> 1. Load compressed matrix from directory /home/imman/.local/share/R/BPCells/demo_data/demo_mat_filtered_subsetted
#> 2. Select rows: 1, 2 and cols: 1, 2


#######################################################################
## as(bpcells_mat, "dgCMatrix") example
#######################################################################
mat_dgc <- as(mat, "dgCMatrix")
mat_dgc
#> 2 x 2 sparse Matrix of class "dgCMatrix"
#>                 TTTAGCAAGGTAGCTT-1 AGCCGGTTCCGGAACC-1
#> ENSG00000272602                  1                  .
#> ENSG00000250312                  .                  .


## as.matrix(bpcells_mat) example
as.matrix(mat)
#>                 TTTAGCAAGGTAGCTT-1 AGCCGGTTCCGGAACC-1
#> ENSG00000272602                  1                  0
#> ENSG00000250312                  0                  0

## Alternatively, can also use function as()
as(mat, "matrix")
#>                 TTTAGCAAGGTAGCTT-1 AGCCGGTTCCGGAACC-1
#> ENSG00000272602                  1                  0
#> ENSG00000250312                  0                  0

#######################################################################
## as(dgc_mat, "IterableMatrix") example
#######################################################################
as(mat_dgc, "IterableMatrix")
#> 2 x 2 IterableMatrix object with class Iterable_dgCMatrix_wrapper
#> 
#> Row names: ENSG00000272602, ENSG00000250312
#> Col names: TTTAGCAAGGTAGCTT-1, AGCCGGTTCCGGAACC-1
#> 
#> Data type: double
#> Storage order: column major
#> 
#> Queued Operations:
#> 1. Load dgCMatrix from memory