| Environment | Status |
|---|---|
| BioC-release |  |
| BioC-devel |  |
The alabaster.ranges package implements methods for saving and loading GRanges and GRangesList objects under the alabaster framework.
It provides a language-agnostic method for serializing genomic coordinates in these objects, as well as data in related objects like compressed lists.
To get started, install the package and its dependencies from Bioconductor:
# install.packages("BiocManager")
BiocManager::install("alabaster.ranges")We can then save a GRanges to a file, preserving its metadata and mcols:
library(GenomicRanges)
gr <- GRanges("chrA", IRanges(sample(100), width=sample(100)))
mcols(gr)$score <- runif(length(gr))
metadata(gr)$genome <- "Aaron"
library(alabaster.ranges)
tmp <- tempfile()
saveObject(gr, tmp)
roundtrip <- loadObject(tmp)
class(roundtrip)
## [1] "GRanges"
## attr(,"package")
## [1] "GenomicRanges"Same for a GRangesList to a file:
exons <- GRanges("chrA", IRanges(sample(100), width=sample(100)))
genes <- split(exons, sample(LETTERS, 100, replace=TRUE))
mcols(genes)$score <- runif(length(genes))
metadata(genes)$genome <- "Aaron"
library(alabaster.ranges)
tmp <- tempfile()
saveObject(genes, tmp)
roundtrip <- loadObject(tmp)
class(roundtrip)
## [1] "CompressedGRangesList"
## attr(,"package")
## [1] "GenomicRanges"