The alabaster.string package implements methods for saving and loading XStringSet objects under the alabaster framework. It provides a language-agnostic method for serializing biological sequences along with any sequence-specific metadata. To get started, install the package and its dependencies from Bioconductor:
# install.packages("BiocManager")
BiocManager::install("alabaster.string")
In the example below, we save a QualityScaledDNAStringSet object to file:
library(Biostrings) example(QualityScaledDNAStringSet, echo=FALSE) # can't be bothered to copy it here. qdna1 ## A QualityScaledDNAStringSet instance containing: ## ## DNAStringSet object of length 2: ## width seq ## [1] 4 TTGA ## [2] 4 CTCN ## ## PhredQuality object of length 2: ## width seq ## [1] 4 *+,- ## [2] 4 6789 library(alabaster.string) tmp <- tempfile() saveObject(qdna1, tmp) roundtrip <- readObject(tmp) class(roundtrip) ## [1] "QualityScaledDNAStringSet" ## attr(,"package") ## [1] "Biostrings"
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