beachmat.tiledb provides a C++ API to extract numeric data from TileDB-backed matrices from the TileDBArray package. This extends the beachmat package to the matrix representations in the tatami_tiledb library. By including this package, users and developers can enable tatami-compatible C++ code to operate natively on file-backed data via the TileDB C library.
Users can simply load the package in their R session:
This will automatically extend beachmat’s functionality to TileDBArray matrices. Any package code based on beachmat will now be able to access TileDB data natively without any further work.
Developers should read the beachmat developer guide if they have not done so already.
Developers can import beachmat.tiledb
in their packages to guarantee native support for TileDBArray
classes. This registers more initializeCpp() methods that
initializes the appropriate C++ representations for these classes. Of
course, this adds some more dependencies to the package, which may or
may not be acceptable; some developers may prefer to leave this choice
to the user or hide it behind an optional parameter to reduce the
installation burden (e.g., if TileDB-backed matrices are not expected to
be a common input in the package workflow).
It’s worth noting that beachmat
by itself will already work with TileDBMatrix objects even
without loading beachmat.tiledb.
However, this is not as efficient as any package C++ code needs to go
back into R to extract the matrix data via
DelayedArray::extract_array() and friends. Importing beachmat.tiledb
provides native support without the need for calls to R functions.
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] beachmat.tiledb_0.99.1 knitr_1.49 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9
## [4] crayon_1.5.3 compiler_4.4.2 BiocManager_1.30.25
## [7] Rcpp_1.0.13-1 nanoarrow_0.6.0 jquerylib_0.1.4
## [10] IRanges_2.41.2 yaml_2.3.10 fastmap_1.2.0
## [13] lattice_0.22-6 XVector_0.47.1 R6_2.5.1
## [16] RcppCCTZ_0.2.13 S4Arrays_1.7.1 generics_0.1.3
## [19] tiledb_0.30.2 BiocGenerics_0.53.3 RcppSpdlog_0.0.19
## [22] DelayedArray_0.33.3 MatrixGenerics_1.19.0 maketools_1.3.1
## [25] TileDBArray_1.17.0 bslib_0.8.0 rlang_1.1.4
## [28] cachem_1.1.0 xfun_0.49 sass_0.4.9
## [31] sys_3.4.3 bit64_4.5.2 SparseArray_1.7.2
## [34] cli_3.6.3 spdl_0.0.5 digest_0.6.37
## [37] grid_4.4.2 lifecycle_1.0.4 S4Vectors_0.45.2
## [40] evaluate_1.0.1 nanotime_0.3.10 buildtools_1.0.0
## [43] zoo_1.8-12 beachmat_2.23.5 abind_1.4-8
## [46] stats4_4.4.2 rmarkdown_2.29 matrixStats_1.4.1
## [49] tools_4.4.2 htmltools_0.5.8.1