GSE280465 provides access to processed adult DNA methylation data derived
from GEO accession
GSE280465.
The source data were generated on GPL33022, the Illumina Infinium
MethylationEPIC version 2 array.
The ExperimentHub resource is a RangedSummarizedExperiment with beta, M, and
CN assays for 163 adult samples from 47 individuals. Samples represent buccal,
saliva, dried blood spot, and peripheral blood mononuclear cell tissues.
Genomic ranges use hg38 coordinates.
The source publication is:
Apsley AT, Ye Q, Caspi A, Chiaro C, Etzel L, Hastings WJ, Heim CM, Kozlosky J, Noll JG, Schreier HMC, Shenk CE, Sugden K, Shalev I. Cross-tissue comparison of epigenetic aging clocks in humans. Aging Cell. 2025;24(4):e14451. doi:10.1111/acel.14451.
The data can be located in ExperimentHub using the GEO accession or the
package name. The loaded object can then be inspected with standard
SummarizedExperiment accessors.
library(ExperimentHub)
library(GSE280465)
library(SummarizedExperiment)
eh <- ExperimentHub()
query(eh, "GSE280465")
se <- GSE280465()
se
se <- GSE280465_GPL33022_EPICv2()
dim(se)
assayNames(se)
colData(se)
rowRanges(se)
metadata(se)The package metadata describe the hosted resource and its source.
metadataFile <- system.file("extdata", "metadata.csv", package = "GSE280465")
metadata <- utils::read.csv(metadataFile, stringsAsFactors = FALSE)
metadata[, c("Title", "Genome", "SourceType", "RDataClass", "DispatchClass")]## Title Genome SourceType RDataClass
## 1 GSE280465_GPL33022_EPICv2 hg38 IDAT RangedSummarizedExperiment
## DispatchClass
## 1 RdsThe serialized RangedSummarizedExperiment is hosted on Zenodo:
paste0(metadata$Location_Prefix, metadata$RDataPath)## [1] "https://zenodo.org/records/21200586/files/GSE280465_GPL33022_EPICv2.rds"sessionInfo()## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.24-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] BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.39 R6_2.6.1 bookdown_0.47
## [4] fastmap_1.2.0 xfun_0.60 cachem_1.1.0
## [7] knitr_1.51 htmltools_0.5.9 rmarkdown_2.31
## [10] lifecycle_1.0.5 cli_3.6.6 sass_0.4.10
## [13] jquerylib_0.1.4 compiler_4.6.1 tools_4.6.1
## [16] evaluate_1.0.5 bslib_0.11.0 yaml_2.3.12
## [19] otel_0.2.0 BiocManager_1.30.27 jsonlite_2.0.0
## [22] rlang_1.3.0