| Environment | Status |
|---|---|
| BioC-release |  |
| BioC-devel |  |
The alabaster.se package implements methods for saving and loading SummarizedExperiment objects under the alabaster framework.
It provides a language-agnostic method for serializing experimental data and annotations in these objects, including the genomic coordinates in a RangedSummarizedExperiment.
To get started, install the package and its dependencies from Bioconductor:
# install.packages("BiocManager")
BiocManager::install("alabaster.se")In the example below, we save a RangedSummarizedExperiment object to file:
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)
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "RangedSummarizedExperiment"
## attr(,"package")
## [1] "SummarizedExperiment"