Contents

1 Overview

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.

2 Quick start

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"            "_environment.json" "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.

3 Saving delayed operations

For DelayedArrays, we may instead choose to save the delayed operations themselves to file. This creates a HDF5 file following the chihaya format, containing the delayed operations rather than the results of their evaluation.

library(DelayedArray)
y <- DelayedArray(rsparsematrix(1000, 100, 0.05))
y <- log1p(abs(y) / 1:100) # adding some delayed ops.

tmp <- tempfile()
saveObject(y, tmp, DelayedArray.preserve.ops=TRUE)

# Inspecting the HDF5 file reveals many delayed operations:
rhdf5::h5ls(file.path(tmp, "array.h5"))
##                            group          name       otype  dclass   dim
## 0                              / delayed_array   H5I_GROUP              
## 1                 /delayed_array        method H5I_DATASET  STRING ( 0 )
## 2                 /delayed_array          seed   H5I_GROUP              
## 3            /delayed_array/seed         along H5I_DATASET INTEGER ( 0 )
## 4            /delayed_array/seed        method H5I_DATASET  STRING ( 0 )
## 5            /delayed_array/seed          seed   H5I_GROUP              
## 6       /delayed_array/seed/seed        method H5I_DATASET  STRING ( 0 )
## 7       /delayed_array/seed/seed          seed   H5I_GROUP              
## 8  /delayed_array/seed/seed/seed     by_column H5I_DATASET INTEGER ( 0 )
## 9  /delayed_array/seed/seed/seed          data H5I_DATASET   FLOAT  5000
## 10 /delayed_array/seed/seed/seed      dimnames   H5I_GROUP              
## 11 /delayed_array/seed/seed/seed       indices H5I_DATASET INTEGER  5000
## 12 /delayed_array/seed/seed/seed        indptr H5I_DATASET INTEGER   101
## 13 /delayed_array/seed/seed/seed         shape H5I_DATASET INTEGER     2
## 14           /delayed_array/seed          side H5I_DATASET  STRING ( 0 )
## 15           /delayed_array/seed         value H5I_DATASET INTEGER  1000
# And indeed, we can recover those same operations.
readObject(tmp)
## <1000 x 100> sparse ReloadedMatrix object of type "double":
##           [,1]   [,2]   [,3] ...       [,99]      [,100]
##    [1,]      0      0      0   . 0.000000000 0.000000000
##    [2,]      0      0      0   . 0.000000000 0.000000000
##    [3,]      0      0      0   . 0.000000000 0.000000000
##    [4,]      0      0      0   . 0.008711941 0.000000000
##    [5,]      0      0      0   . 0.000000000 0.000000000
##     ...      .      .      .   .           .           .
##  [996,]      0      0      0   . 0.000000000 0.000000000
##  [997,]      0      0      0   . 0.000000000 0.000000000
##  [998,]      0      0      0   . 0.000000000 0.000000000
##  [999,]      0      0      0   . 0.003831036 0.000000000
## [1000,]      0      0      0   . 0.000000000 0.022739487

This allows users to avoid evaluation of the operations when saving objects, which may improve efficiency, e.g., by avoiding loss of sparsity or casting to a larger type.

Session information

sessionInfo()
## R version 4.6.0 RC (2026-04-17 r89917)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## 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       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] DelayedArray_0.38.0     SparseArray_1.12.0      S4Arrays_1.12.0        
##  [4] abind_1.4-8             IRanges_2.46.0          S4Vectors_0.50.0       
##  [7] MatrixGenerics_1.24.0   matrixStats_1.5.0       BiocGenerics_0.58.0    
## [10] generics_0.1.4          alabaster.matrix_1.12.0 alabaster.base_1.12.0  
## [13] Matrix_1.7-5            BiocStyle_2.40.0       
## 
## loaded via a namespace (and not attached):
##  [1] jsonlite_2.0.0           compiler_4.6.0           BiocManager_1.30.27     
##  [4] Rcpp_1.1.1-1.1           rhdf5filters_1.24.0      jquerylib_0.1.4         
##  [7] yaml_2.3.12              fastmap_1.2.0            lattice_0.22-9          
## [10] R6_2.6.1                 XVector_0.52.0           knitr_1.51              
## [13] bookdown_0.46            h5mread_1.4.0            bslib_0.10.0            
## [16] rlang_1.2.0              cachem_1.1.0             HDF5Array_1.40.0        
## [19] xfun_0.57                sass_0.4.10              otel_0.2.0              
## [22] cli_3.6.6                Rhdf5lib_2.0.0           digest_0.6.39           
## [25] grid_4.6.0               alabaster.schemas_1.12.0 rhdf5_2.56.0            
## [28] lifecycle_1.0.5          evaluate_1.0.5           rmarkdown_2.31          
## [31] tools_4.6.0              htmltools_0.5.9