---
title: Saving `SummarizedExperiment`s to artifacts and back again
author:
- name: Aaron Lun
  email: infinite.monkeys.with.keyboards@gmail.com
package: alabaster.se
date: "Revised: September 22, 2022"
output:
  BiocStyle::html_document
vignette: >
  %\VignetteIndexEntry{Saving and loading SummarizedExperiments}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, echo=FALSE}
library(BiocStyle)
self <- Biocpkg("alabaster.se")
knitr::opts_chunk$set(error=FALSE, warning=FALSE, message=FALSE)
```

# Overview 

The `r self` package implements methods to save `SummarizedExperiment` objects to file artifacts and load them back into R.
Check out the `r Biocpkg("alabaster.base")` for more details on the motivation and concepts of the **alabaster** framework.

# Quick start

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

```{r}
# Example taken from ?SummarizedExperiment
library(SummarizedExperiment)
nrows <- 200
ncols <- 6
counts <- matrix(rpois(nrows * ncols, 10), nrows, ncols)
rowRanges <- GRanges(
    rep(c("chr1", "chr2"), c(50, 150)),
    IRanges(floor(runif(200, 1e5, 1e6)), width=100),
    strand=sample(c("+", "-"), 200, TRUE)
)
colData <- DataFrame(
    Treatment=rep(c("ChIP", "Input"), 3), 
    row.names=LETTERS[1:6]
)
rse <- SummarizedExperiment(
    assays=SimpleList(counts=counts),
    rowRanges=rowRanges, 
    colData=colData
)
rownames(rse) <- sprintf("GENE_%03d", 1:200)
rse

library(alabaster.se)
tmp <- tempfile()
saveObject(rse, tmp)

list.files(tmp, recursive=TRUE)
```

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

```{r}
roundtrip <- readObject(tmp)
roundtrip
```

# Session information {-}

```{r}
sessionInfo()
```