RBedMethyl provides disk-backed access to nanoporetech modkit bedMethyl files generated from ONT data, enabling ONT-scale workflows without loading full tables into memory. This vignette demonstrates a typical workflow: ingest, subset by region, compute per-region summaries, and coerce to downstream Bioconductor classes.
# Example bedMethyl-like content (small for illustration; headerless)
lines <- c(
paste("chr1", 0, 1, "m", 0, "+", 0, 1, 0, 10, 0.5, 5, 5, 0, 0, 0, 0, 0, sep = "\t"),
paste("chr1", 10, 11, "m", 0, "+", 10, 11, 0, 20, 0.25, 5, 15, 0, 0, 0, 0, 0, sep = "\t"),
paste("chr2", 0, 1, "m", 0, "-", 0, 1, 0, 8, 0.375, 3, 5, 0, 0, 0, 0, 0, sep = "\t")
)
bed <- tempfile(fileext = ".bed")
writeLines(lines, bed)
bm <- readBedMethyl(bed, mod = "m", fields = c("coverage", "pct", "mod_reads"))
bm
#> An object of class "RBedMethyl"
#> Slot "assays":
#> List of length 7
#> names(7): chrom chromStart chromEnd strand coverage pct mod_reads
#>
#> Slot "chrom_levels":
#> [1] "chr1" "chr2"
#>
#> Slot "strand_levels":
#> [1] "+" "-"
#>
#> Slot "chr_index":
#> starts ends
#> chr1 1 2
#> chr2 3 3
#>
#> Slot "index":
#> [1] 1 2 3
#>
#> Slot "mod":
#> [1] "m"regions <- GenomicRanges::GRanges(
seqnames = c("chr1", "chr2"),
ranges = IRanges::IRanges(start = c(1, 1), end = c(12, 2))
)
summarizeByRegion(bm, regions)
#> DataFrame with 2 rows and 4 columns
#> coverage mod_reads beta n_sites
#> <numeric> <numeric> <numeric> <integer>
#> 1 30 10 0.333333 2
#> 2 8 3 0.375000 1# RangedSummarizedExperiment
rse <- as(bm, "RangedSummarizedExperiment")
rse
#> class: RangedSummarizedExperiment
#> dim: 3 1
#> metadata(0):
#> assays(3): coverage mod_reads pct
#> rownames: NULL
#> rowData names(0):
#> colnames: NULL
#> colData names(0):
# bsseq (if installed)
if (requireNamespace("bsseq", quietly = TRUE) &&
methods::hasMethod("coerce", c("RBedMethyl", "BSseq"))) {
bs <- as(bm, "BSseq")
bs
} else {
message("bsseq is not installed or BSseq coercion is unavailable; skipping BSseq coercion.")
}
#> An object of type 'BSseq' with
#> 3 methylation loci
#> 1 samples
#> has not been smoothed
#> All assays are in-memorysessionInfo()
#> R Under development (unstable) (2026-03-05 r89546)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] RBedMethyl_0.99.0 BiocStyle_2.39.0
#>
#> loaded via a namespace (and not attached):
#> [1] SummarizedExperiment_1.41.1 rjson_0.2.23
#> [3] xfun_0.56 bslib_0.10.0
#> [5] rhdf5_2.55.13 Biobase_2.71.0
#> [7] lattice_0.22-9 bitops_1.0-9
#> [9] rhdf5filters_1.23.3 tools_4.6.0
#> [11] generics_0.1.4 curl_7.0.0
#> [13] stats4_4.6.0 parallel_4.6.0
#> [15] R.oo_1.27.1 Matrix_1.7-4
#> [17] data.table_1.18.2.1 BSgenome_1.79.1
#> [19] RColorBrewer_1.1-3 cigarillo_1.1.0
#> [21] S4Vectors_0.49.0 sparseMatrixStats_1.23.0
#> [23] lifecycle_1.0.5 compiler_4.6.0
#> [25] farver_2.1.2 Rsamtools_2.27.1
#> [27] Biostrings_2.79.5 statmod_1.5.1
#> [29] Seqinfo_1.1.0 codetools_0.2-20
#> [31] permute_0.9-10 htmltools_0.5.9
#> [33] sass_0.4.10 RCurl_1.98-1.17
#> [35] yaml_2.3.12 crayon_1.5.3
#> [37] jquerylib_0.1.4 R.utils_2.13.0
#> [39] BiocParallel_1.45.0 DelayedArray_0.37.0
#> [41] cachem_1.1.0 limma_3.67.0
#> [43] abind_1.4-8 gtools_3.9.5
#> [45] locfit_1.5-9.12 digest_0.6.39
#> [47] restfulr_0.0.16 bookdown_0.46
#> [49] fastmap_1.2.0 grid_4.6.0
#> [51] cli_3.6.5 SparseArray_1.11.11
#> [53] S4Arrays_1.11.1 XML_3.99-0.22
#> [55] dichromat_2.0-0.1 h5mread_1.3.2
#> [57] DelayedMatrixStats_1.33.0 scales_1.4.0
#> [59] httr_1.4.8 rmarkdown_2.30
#> [61] XVector_0.51.0 matrixStats_1.5.0
#> [63] otel_0.2.0 R.methodsS3_1.8.2
#> [65] beachmat_2.27.3 HDF5Array_1.39.0
#> [67] evaluate_1.0.5 knitr_1.51
#> [69] BiocIO_1.21.0 GenomicRanges_1.63.1
#> [71] IRanges_2.45.0 rtracklayer_1.71.3
#> [73] rlang_1.1.7 Rcpp_1.1.1
#> [75] glue_1.8.0 BiocManager_1.30.27
#> [77] BiocGenerics_0.57.0 bsseq_1.47.1
#> [79] jsonlite_2.0.0 R6_2.6.1
#> [81] Rhdf5lib_1.33.0 GenomicAlignments_1.47.0
#> [83] MatrixGenerics_1.23.0