Bioconductor software packages are
capped at 5 MB per file. Eight of the data layers behind the
cpgdirection package are larger than that, so they live
here, on ExperimentHub, and are fetched on first use – then cached
locally, so the download cost is paid once per machine.
Most users never call this package directly:
cpgdirection resolves every layer through its data backend,
using a bundled copy when one is installed and falling back to these Hub
resources otherwise.
## Loading required package: ExperimentHub## Loading required package: BiocGenerics## Loading required package: generics##
## Attaching package: 'generics'## The following objects are masked from 'package:base':
##
## as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
## setequal, union##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs## The following object is masked from 'package:utils':
##
## data## The following objects are masked from 'package:base':
##
## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, saveRDS, scale, sequence, table,
## tapply, transform, unique, unsplit, which.max, which.min## Loading required package: AnnotationHub## Loading required package: BiocFileCache## Loading required package: dbplyr## name genome
## 1 lookup_blood_hg19 hg19
## 2 lookup_nasal_epithelium_hg19 hg19
## 3 lookup_solid_tissue_hg19 hg19
## 4 smr_directions hg19
## 5 cpg_positions_hg19 hg19
## 6 brain_directions hg19
## 7 saliva_bridge_scores hg19
## 8 epicv2_probe_gene_annotation hg38Direct retrieval from the Hub (cached after the first download):
Air-gapped machines, containers without network access, and analyses that must pin an exact data snapshot can serve the same files from a local directory instead of the Hub. The chunk below demonstrates the mechanism with a stand-in file, so it runs anywhere:
d <- tempfile()
dir.create(d)
saveRDS(data.frame(cpg_id = "cg00000029", chr = "chr16", pos = 53434200L),
file.path(d, "cpg_positions_hg19.rds"))
old <- options(cpgdirectionData.local = d)
head(getCpgPositionsHg19())## cpg_id chr pos
## 1 cg00000029 chr16 53434200Every resource is built by inst/scripts/make-data.R from
the full cpgdirection build. The resources themselves are archived on
Zenodo (DOI 10.5281/zenodo.22225164)
and retrieved from there by ExperimentHub. The multi-source EPIC v2
probe-to-gene annotation is the union of five independent tracks
(Illumina EPIC-8v2-0_A2 manifest UCSC RefGene and GencodeV41; the Zhou
lab SeSAMe GENCODE v41 annotation; the Exeter GENCODE 47 re-annotation,
Zenodo record 15181885, including its regulatory-element assignments),
with per-track support flags so downstream consumers can weight
assignments by agreement.
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [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: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] cpgdirectionData_0.99.1 ExperimentHub_3.3.2 AnnotationHub_4.3.2
## [4] BiocFileCache_3.3.0 dbplyr_2.6.0 BiocGenerics_0.59.12
## [7] generics_0.1.4 rmarkdown_2.32
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.4 sass_0.4.10 BiocVersion_3.24.0
## [4] RSQLite_3.53.3 digest_0.6.39 magrittr_2.0.5
## [7] evaluate_1.0.5 fastmap_1.2.0 blob_1.3.0
## [10] jsonlite_2.0.0 AnnotationDbi_1.75.2 DBI_1.3.0
## [13] BiocManager_1.30.27 httr_1.4.9 Biostrings_2.81.9
## [16] httr2_1.3.0 jquerylib_0.1.4 cli_3.6.6
## [19] crayon_1.5.3 rlang_1.3.0 XVector_0.53.0
## [22] Biobase_2.73.2 bit64_4.8.6 cachem_1.1.0
## [25] yaml_2.3.12 BiocBaseUtils_1.15.1 otel_0.2.0
## [28] tools_4.6.1 memoise_2.0.1 dplyr_1.2.1
## [31] filelock_1.0.3 curl_8.0.0 png_0.1-9
## [34] buildtools_1.0.0 vctrs_0.7.3 R6_2.6.1
## [37] stats4_4.6.1 lifecycle_1.0.5 Seqinfo_1.3.2
## [40] KEGGREST_1.53.6 S4Vectors_0.51.10 IRanges_2.47.5
## [43] bit_4.6.0 pkgconfig_2.0.3 pillar_1.11.1
## [46] bslib_0.12.0 glue_1.8.1 xfun_0.61
## [49] tibble_3.3.1 tidyselect_1.2.1 sys_3.4.3
## [52] knitr_1.52 htmltools_0.5.9 maketools_1.3.2
## [55] compiler_4.6.1