Matter 2 provides an updated and more robust C++ backend to matter objects, along with a completely new implementation of sparse arrays and new signal processing functions for nonuniform sparse signal data.
Originally designed as a backend for the Cardinal package, The first version of Matter was constantly evolving to handle the ever-increasing demands of larger-than-memory mass spectrometry (MS) imaging experiments. While it was designed to be flexible from a user’s point-of-view to handle a wide array for file structures beyond the niche of MS imaging, its codebase was becoming increasingly difficult to maintain and update.
Matter 2 was re-written from the ground up to simplify some features that were rarely needed in practice and to provide a more robust and future-proof codebase for further improvement.
Matter can be installed via the BiocManager package.
install.packages("BiocManager")
BiocManager::install("matter")The same function can be used to update Matter and other Bioconductor packages.
Once installed, Matter can be loaded with library():
library(matter)Coming soon…..
Coming soon…..
Coming soon…..
sessionInfo()## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB 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
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] matter_2.0.0 Matrix_1.5-1 BiocParallel_1.32.0
## [4] BiocStyle_2.26.0
##
## loaded via a namespace (and not attached):
## [1] knitr_1.40 magrittr_2.0.3 BiocGenerics_0.44.0
## [4] lattice_0.20-45 R6_2.5.1 rlang_1.0.6
## [7] fastmap_1.1.0 stringr_1.4.1 tools_4.2.1
## [10] parallel_4.2.1 grid_4.2.1 biglm_0.9-2.1
## [13] xfun_0.34 irlba_2.3.5.1 DBI_1.1.3
## [16] cli_3.4.1 jquerylib_0.1.4 ProtGenerics_1.30.0
## [19] htmltools_0.5.3 yaml_2.3.6 digest_0.6.30
## [22] bookdown_0.29 BiocManager_1.30.19 sass_0.4.2
## [25] codetools_0.2-18 cachem_1.0.6 evaluate_0.17
## [28] rmarkdown_2.17 stringi_1.7.8 compiler_4.2.1
## [31] bslib_0.4.0 jsonlite_1.8.3