alabaster.matrix 1.6.1
The alabaster.matrix package implements methods to save matrix-like objects to file artifacts and load them back into R. Check out the alabaster.base for more details on the motivation and the alabaster framework.
Given an array-like object, we can use saveObject()
to save it inside a staging directory:
library(Matrix)
y <- rsparsematrix(1000, 100, density=0.05)
library(alabaster.matrix)
tmp <- tempfile()
saveObject(y, tmp)
list.files(tmp, recursive=TRUE)
## [1] "OBJECT" "matrix.h5"
We then load it back into our R session with loadObject()
.
This creates a HDF5-backed S4 array that can be easily coerced into the desired format, e.g., a dgCMatrix
.
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "ReloadedMatrix"
## attr(,"package")
## [1] "alabaster.matrix"
This process is supported for all base arrays, Matrix objects and DelayedArray objects.
🚧🚧🚧 Oops. Yet to migrate the delayed operations to the new saveObject
/readObject
world - stay tuned. 🚧🚧🚧
sessionInfo()
## R version 4.4.2 (2024-10-31)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] alabaster.matrix_1.6.1 alabaster.base_1.6.1 Matrix_1.7-1
## [4] BiocStyle_2.34.0
##
## loaded via a namespace (and not attached):
## [1] jsonlite_1.8.9 compiler_4.4.2 BiocManager_1.30.25
## [4] crayon_1.5.3 Rcpp_1.0.13-1 rhdf5filters_1.18.0
## [7] jquerylib_0.1.4 IRanges_2.40.0 yaml_2.3.10
## [10] fastmap_1.2.0 lattice_0.22-6 R6_2.5.1
## [13] XVector_0.46.0 S4Arrays_1.6.0 knitr_1.49
## [16] BiocGenerics_0.52.0 DelayedArray_0.32.0 bookdown_0.41
## [19] MatrixGenerics_1.18.0 bslib_0.8.0 rlang_1.1.4
## [22] cachem_1.1.0 HDF5Array_1.34.0 xfun_0.49
## [25] sass_0.4.9 SparseArray_1.6.0 cli_3.6.3
## [28] Rhdf5lib_1.28.0 zlibbioc_1.52.0 digest_0.6.37
## [31] grid_4.4.2 alabaster.schemas_1.6.0 rhdf5_2.50.0
## [34] lifecycle_1.0.4 S4Vectors_0.44.0 evaluate_1.0.1
## [37] abind_1.4-8 stats4_4.4.2 rmarkdown_2.29
## [40] matrixStats_1.4.1 tools_4.4.2 htmltools_0.5.8.1