Contents

1 Overview

The alabaster.se package implements methods to save SummarizedExperiment objects to file artifacts and load them back into R. Check out the alabaster.base for more details on the motivation and concepts of the alabaster framework.

2 Quick start

Given a (Ranged)SummarizedExperiment, we can use saveObject() to save it inside a staging directory:

library(SummarizedExperiment)
example(SummarizedExperiment, echo=FALSE) # can't be bothered to copy it here.
rse
## class: RangedSummarizedExperiment 
## dim: 200 6 
## metadata(0):
## assays(1): counts
## rownames: NULL
## rowData names(1): feature_id
## colnames(6): A B ... E F
## colData names(1): Treatment
library(alabaster.se)
tmp <- tempfile()
saveObject(rse, tmp)

list.files(tmp, recursive=TRUE)
##  [1] "OBJECT"                                 
##  [2] "assays/0/OBJECT"                        
##  [3] "assays/0/array.h5"                      
##  [4] "assays/names.json"                      
##  [5] "column_data/OBJECT"                     
##  [6] "column_data/basic_columns.h5"           
##  [7] "row_data/OBJECT"                        
##  [8] "row_data/basic_columns.h5"              
##  [9] "row_ranges/OBJECT"                      
## [10] "row_ranges/ranges.h5"                   
## [11] "row_ranges/sequence_information/OBJECT" 
## [12] "row_ranges/sequence_information/info.h5"

We can then load it back into the session with readObject().

roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "RangedSummarizedExperiment"
## attr(,"package")
## [1] "SummarizedExperiment"

Session information

sessionInfo()
## R version 4.4.0 (2024-04-24 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows Server 2022 x64 (build 20348)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=C                          
## [2] LC_CTYPE=English_United States.utf8   
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.utf8    
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] alabaster.se_1.4.1          alabaster.base_1.4.1       
##  [3] SummarizedExperiment_1.34.0 Biobase_2.64.0             
##  [5] GenomicRanges_1.56.0        GenomeInfoDb_1.40.0        
##  [7] IRanges_2.38.0              S4Vectors_0.42.0           
##  [9] BiocGenerics_0.50.0         MatrixGenerics_1.16.0      
## [11] matrixStats_1.3.0           BiocStyle_2.32.0           
## 
## loaded via a namespace (and not attached):
##  [1] Matrix_1.7-0            jsonlite_1.8.8          compiler_4.4.0         
##  [4] BiocManager_1.30.23     crayon_1.5.2            Rcpp_1.0.12            
##  [7] rhdf5filters_1.16.0     alabaster.matrix_1.4.0  jquerylib_0.1.4        
## [10] yaml_2.3.8              fastmap_1.2.0           lattice_0.22-6         
## [13] R6_2.5.1                XVector_0.44.0          S4Arrays_1.4.1         
## [16] knitr_1.46              DelayedArray_0.30.1     bookdown_0.39          
## [19] GenomeInfoDbData_1.2.12 bslib_0.7.0             rlang_1.1.3            
## [22] HDF5Array_1.32.0        cachem_1.1.0            xfun_0.44              
## [25] alabaster.ranges_1.4.1  sass_0.4.9              SparseArray_1.4.5      
## [28] cli_3.6.2               Rhdf5lib_1.26.0         zlibbioc_1.50.0        
## [31] digest_0.6.35           grid_4.4.0              alabaster.schemas_1.4.0
## [34] rhdf5_2.48.0            lifecycle_1.0.4         evaluate_0.23          
## [37] abind_1.4-5             rmarkdown_2.27          httr_1.4.7             
## [40] tools_4.4.0             htmltools_0.5.8.1       UCSC.utils_1.0.0