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The major outputs from the extraction module are R objects from the bsseq Bioconductor package, which contain methylation proportion and coverage information at all cytosine loci in the human genome. bsseq extends the SummarizedExperiment class, which provides a general and popular format for storing genomics data and is memory efficient thanks to the HDF5Array backend. Two bsseq objects are produced, with one object containing cytosine sites in CpG context, and the other containing the remaining CpH loci

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