Save common bioinformatics file formats

Environment	Status
BioC-release
BioC-devel

The alabaster.files package implements methods for processing common bioinformatics file formats (e.g., BAM, GFF, BED) in the alabaster framework. This allows users to store these files as part of larger Bioconductor objects, e.g., by embedding them inside the metadata() field of a SummarizedExperiment. To get started, install the package and its dependencies from Bioconductor:

# install.packages("BiocManager")
BiocManager::install("alabaster.files")

We can then assemble complex objects containing various files:

library(alabaster.files)
library(S4Vectors)
df <- DataFrame(Sample=LETTERS[1:4])

# Adding a column of assorted wrapper files:
df$File <- list(
    BamFileReference(system.file("extdata", "ex1.bam", package="Rsamtools")),
    BigWigFileReference(system.file("tests", "test.bw", package = "rtracklayer")),
    BigBedFileReference(system.file("tests", "test.bb", package = "rtracklayer")),
    BcfFileReference(system.file("extdata", "ex1.bcf.gz", package = "Rsamtools"))
)

# Saving it all to the staging directory:
dir <- tempfile()
saveObject(df, dir)

When we load the parent DataFrame back into the R session, we have references to copies of the files in the staging directory. Users can inspect the path from each *Reference for further analysis.

roundtrip <- readObject(dir)
roundtrip$File
## [[1]]
## BamFileReference object
## path: /tmp/RtmpdTiBzJ/file136647b568cb/other_columns/1/other_contents/0/file.bam
## index: NULL
## 
## [[2]]
## BigWigFileReference object
## path: /tmp/RtmpdTiBzJ/file136647b568cb/other_columns/1/other_contents/1/file.bw
## 
## [[3]]
## BigBedFileReference object
## path: /tmp/RtmpdTiBzJ/file136647b568cb/other_columns/1/other_contents/2/file.bb
## 
## [[4]]
## BcfFileReference object
## path: /tmp/RtmpdTiBzJ/file136647b568cb/other_columns/1/other_contents/3/file.bcf
## index: NULL