| Environment | Status |
|---|---|
| BioC-release |  |
| BioC-devel |  |
The alabaster.bumpy package implements methods for saving and loading BumpyMatrix objects under the alabaster framework.
It provides a language-agnostic method for serializing data in bumpy matrices, most typically as assays of a SummarizedExperiment.
To get started, install the package and its dependencies from Bioconductor:
# install.packages("BiocManager")
BiocManager::install("alabaster.bumpy")Let's create a BumpyMatrix object:
library(BumpyMatrix)
library(S4Vectors)
df <- DataFrame(x=runif(100), y=runif(100))
f <- factor(sample(letters[1:20], nrow(df), replace=TRUE), letters[1:20])
mat <- BumpyMatrix(split(df, f), c(5, 4))We save it to file:
library(alabaster.bumpy)
tmp <- tempfile()
saveObject(mat, tmp)
And then load it back:
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "BumpyDataFrameMatrix"
## attr(,"package")
## [1] "BumpyMatrix"