GSE142512 provides access to processed DNA methylation
data derived from GEO accession GSE142512.
The source data include GPL13534 Illumina HumanMethylation450 and
GPL21145 Infinium MethylationEPIC arrays.
The ExperimentHub resources are
RangedSummarizedExperiment objects with beta, M, and CN
assays. The 450K resource contains 485,512 CpG loci across 184 samples
from 84 subjects. The EPIC resource contains 865,859 CpG loci across 211
samples from 90 subjects. Genomic ranges use hg19 coordinates.
The source publication is:
Johnson RK, Vanderlinden LA, Dong F, Carry PM, Seifert J, Waugh K, Shorrosh H, Fingerlin T, Frohnert BI, Yang IV, Kechris K, Rewers M, Norris JM. Longitudinal DNA methylation differences precede type 1 diabetes. Scientific Reports. 2020;10:3721. doi:10.1038/s41598-020-60758-0.
The data can be located in ExperimentHub using the GEO
accession or the package name. The loaded objects can then be inspected
with standard SummarizedExperiment accessors.
library(ExperimentHub)
library(GSE142512)
library(SummarizedExperiment)
eh <- ExperimentHub()
query(eh, "GSE142512")
se450k <- GSE142512(platform = "450K")
seEPIC <- GSE142512(platform = "EPIC")
se450k <- GSE142512_GPL13534_450K()
seEPIC <- GSE142512_GPL21145_EPIC()
dim(se450k)
assayNames(se450k)
colData(se450k)
rowRanges(se450k)
metadata(se450k)The package metadata describe their sources.
metadataFile <- system.file("extdata", "metadata.csv", package = "GSE142512")
metadata <- utils::read.csv(metadataFile, stringsAsFactors = FALSE)
metadata[, c("Title", "Genome", "SourceType", "RDataClass", "DispatchClass")]## Title Genome SourceType RDataClass
## 1 GSE142512_GPL13534_450K hg19 IDAT RangedSummarizedExperiment
## 2 GSE142512_GPL21145_EPIC hg19 IDAT RangedSummarizedExperiment
## DispatchClass
## 1 Rds
## 2 RdsThe serialized RangedSummarizedExperiment objects are
hosted on Zenodo:
## [1] "https://zenodo.org/records/21198533/files/GSE142512_GPL13534_450K.rds"
## [2] "https://zenodo.org/records/21198533/files/GSE142512_GPL21145_EPIC.rds"## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04 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] BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.39 R6_2.6.1 fastmap_1.2.0
## [4] xfun_0.59 maketools_1.3.2 cachem_1.1.0
## [7] knitr_1.51 htmltools_0.5.9 rmarkdown_2.31
## [10] buildtools_1.0.0 lifecycle_1.0.5 cli_3.6.6
## [13] sass_0.4.10 jquerylib_0.1.4 compiler_4.6.1
## [16] sys_3.4.3 tools_4.6.1 bslib_0.11.0
## [19] evaluate_1.0.5 yaml_2.3.12 otel_0.2.0
## [22] BiocManager_1.30.27 jsonlite_2.0.0 rlang_1.2.0