SingleCellExperiments to
artifacts and back againThe alabaster.sce
package implements methods to save SingleCellExperiment
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.
Given a SingleCellExperiment, we can use
saveObject() to save it inside a staging directory:
library(SingleCellExperiment)
mat <- matrix(rpois(10000, 10), ncol=10)
colnames(mat) <- letters[1:10]
rownames(mat) <- sprintf("GENE_%i", seq_len(nrow(mat)))
sce <- SingleCellExperiment(list(counts=mat))
sce$stuff <- LETTERS[1:10]
sce$blah <- runif(10)
reducedDims(sce) <- list(
PCA=matrix(rnorm(ncol(sce)*10), ncol=10),
TSNE=matrix(rnorm(ncol(sce)*2), ncol=2)
)
altExps(sce) <- list(spikes=SummarizedExperiment(list(counts=mat[1:2,])))
sce## class: SingleCellExperiment
## dim: 1000 10
## metadata(0):
## assays(1): counts
## rownames(1000): GENE_1 GENE_2 ... GENE_999 GENE_1000
## rowData names(0):
## colnames(10): a b ... i j
## colData names(2): stuff blah
## reducedDimNames(2): PCA TSNE
## mainExpName: NULL
## altExpNames(1): spikes## [1] "OBJECT"
## [2] "alternative_experiments/0/OBJECT"
## [3] "alternative_experiments/0/assays/0/OBJECT"
## [4] "alternative_experiments/0/assays/0/array.h5"
## [5] "alternative_experiments/0/assays/names.json"
## [6] "alternative_experiments/0/column_data/OBJECT"
## [7] "alternative_experiments/0/column_data/basic_columns.h5"
## [8] "alternative_experiments/0/row_data/OBJECT"
## [9] "alternative_experiments/0/row_data/basic_columns.h5"
## [10] "alternative_experiments/names.json"
## [11] "assays/0/OBJECT"
## [12] "assays/0/array.h5"
## [13] "assays/names.json"
## [14] "column_data/OBJECT"
## [15] "column_data/basic_columns.h5"
## [16] "reduced_dimensions/0/OBJECT"
## [17] "reduced_dimensions/0/array.h5"
## [18] "reduced_dimensions/1/OBJECT"
## [19] "reduced_dimensions/1/array.h5"
## [20] "reduced_dimensions/names.json"
## [21] "row_data/OBJECT"
## [22] "row_data/basic_columns.h5"We can then load it back into the session with
loadObject().
## [1] "SingleCellExperiment"
## attr(,"package")
## [1] "SingleCellExperiment"## R version 4.4.1 (2024-06-14)
## 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] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] alabaster.sce_1.7.0 alabaster.base_1.5.10
## [3] SingleCellExperiment_1.27.2 SummarizedExperiment_1.35.5
## [5] Biobase_2.65.1 GenomicRanges_1.57.2
## [7] GenomeInfoDb_1.41.2 IRanges_2.39.2
## [9] S4Vectors_0.43.2 BiocGenerics_0.51.3
## [11] MatrixGenerics_1.17.1 matrixStats_1.4.1
## [13] BiocStyle_2.33.1
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.9 SparseArray_1.5.45 lattice_0.22-6
## [4] alabaster.se_1.5.4 digest_0.6.37 evaluate_1.0.1
## [7] grid_4.4.1 fastmap_1.2.0 jsonlite_1.8.9
## [10] Matrix_1.7-1 alabaster.schemas_1.5.0 BiocManager_1.30.25
## [13] httr_1.4.7 UCSC.utils_1.1.0 HDF5Array_1.33.8
## [16] jquerylib_0.1.4 abind_1.4-8 cli_3.6.3
## [19] rlang_1.1.4 crayon_1.5.3 XVector_0.45.0
## [22] cachem_1.1.0 DelayedArray_0.31.14 yaml_2.3.10
## [25] S4Arrays_1.5.11 tools_4.4.1 Rhdf5lib_1.27.0
## [28] GenomeInfoDbData_1.2.13 alabaster.ranges_1.5.2 alabaster.matrix_1.5.10
## [31] buildtools_1.0.0 R6_2.5.1 lifecycle_1.0.4
## [34] rhdf5_2.49.0 zlibbioc_1.51.2 bslib_0.8.0
## [37] Rcpp_1.0.13 xfun_0.48 sys_3.4.3
## [40] knitr_1.48 rhdf5filters_1.17.0 htmltools_0.5.8.1
## [43] rmarkdown_2.28 maketools_1.3.1 compiler_4.4.1