| Title: | Data Layers for the cpgdirection Package (ExperimentHub) |
|---|---|
| Description: | ExperimentHub companion to the cpgdirection package. Serves the eight data layers too large to ship inside a Bioconductor software package: the three tissue catalogue lookup tables (blood, nasal epithelium, solid tissue; hg19), the SMR causal-direction table, the EPIC v2 hg19 probe positions, the brain SMR directions, the genome-wide saliva bridge scores, and the multi-source EPIC v2 probe-to-gene annotation (five cross-validated annotation tracks with per-track support flags). Each resource is a serialized data.frame retrieved from ExperimentHub on first use and cached locally thereafter. The cpgdirection package consumes these resources transparently; direct use is possible through the accessors documented here. |
| Authors: | Tsachi Ein-Dor [aut, cre, fnd] (ORCID: <https://orcid.org/0000-0002-3078-7591>) |
| Maintainer: | Tsachi Ein-Dor <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.99.1 |
| Built: | 2026-10-01 12:23:05 UTC |
| Source: | https://github.com/BiocStaging/cpgdirectionData |
Fetches the named resource from ExperimentHub (cached locally by the Hub
after the first download), or from a local directory when
options(cpgdirectionData.local = "<dir>") is set – the directory
must hold the resource as "<name>.rds". The local mode serves
air-gapped machines and lets the cpgdirection stack run against a data
snapshot pinned for a specific analysis.
cpgdData(name)cpgdData(name)
name |
One of |
A data.frame.
# The default retrieval is ExperimentHub (cached after first use): # pos <- cpgdData("cpg_positions_hg19") # The local mode serves the same files from a directory, demonstrated # here with a stand-in so the example runs without network access: 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) pos <- cpgdData("cpg_positions_hg19") head(pos) options(old)# The default retrieval is ExperimentHub (cached after first use): # pos <- cpgdData("cpg_positions_hg19") # The local mode serves the same files from a directory, demonstrated # here with a stand-in so the example runs without network access: 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) pos <- cpgdData("cpg_positions_hg19") head(pos) options(old)
The data layers this package serves
cpgdData_resources()cpgdData_resources()
A data.frame with one row per resource: name (the
identifier accepted by cpgdData), title (the
ExperimentHub title), description and genome.
cpgdData_resources()cpgdData_resources()
ExperimentHub companion to cpgdirection. Bioconductor software
packages are capped at 5 MB per file; the eight data layers served here
are larger than that, so they live on the Hub and are fetched on first
use (then cached locally by ExperimentHub). The cpgdirection
package retrieves them transparently through its data backend; direct
access goes through cpgdData or the named accessors.
Provenance: the layers are built by the scripts under
inst/scripts/ from the sources documented there (the cpgdirection
catalogues and SMR analyses; the Illumina EPIC-8v2-0_A2 manifest; the
Zhou lab SeSAMe EPIC v2 annotation and masks; the Exeter EPIC v2
re-annotation, Zenodo record 15181885; the Garvan EPICv2manifest
cross-hybridization evidence).
Maintainer: Tsachi Ein-Dor [email protected] (ORCID) [funder]
Authors:
Tsachi Ein-Dor [email protected] (ORCID) [funder]
Useful links:
Report bugs at https://github.com/teindor/cpgdirection/issues
Convenience wrappers around cpgdData, one per
resource. getBloodLookup(), getNasalEpitheliumLookup() and
getSolidTissueLookup() return the per-tissue catalogue tables;
getSmrDirections() the SMR causal directions;
getCpgPositionsHg19() the EPIC v2 hg19 probe positions;
getBrainDirections() the brain SMR directions;
getSalivaBridgeScores() the saliva-bridge scores; and
getEpicv2ProbeGeneAnnotation() the multi-source probe-to-gene
annotation.
getBloodLookup() getNasalEpitheliumLookup() getSolidTissueLookup() getSmrDirections() getCpgPositionsHg19() getBrainDirections() getSalivaBridgeScores() getEpicv2ProbeGeneAnnotation()getBloodLookup() getNasalEpitheliumLookup() getSolidTissueLookup() getSmrDirections() getCpgPositionsHg19() getBrainDirections() getSalivaBridgeScores() getEpicv2ProbeGeneAnnotation()
A data.frame; see cpgdData_resources for the
per-resource description.
# Hub retrieval (default): pos <- getCpgPositionsHg19() # Local-mode stand-in so the example runs without network access: 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()) options(old)# Hub retrieval (default): pos <- getCpgPositionsHg19() # Local-mode stand-in so the example runs without network access: 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()) options(old)