Save genomic ranges objects to file

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"

ArtifactDB/alabaster.ranges

Save genomic ranges objects to file