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.
Install GSE142512 from Bioconductor using BiocManager:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GSE142512")
library(GSE142512)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:
paste0(metadata$Location_Prefix, metadata$RDataPath)## [1] "https://zenodo.org/records/21198533/files/GSE142512_GPL13534_450K.rds"
## [2] "https://zenodo.org/records/21198533/files/GSE142512_GPL21145_EPIC.rds"sessionInfo()## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.5 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_0.48
## [4] fastmap_1.2.0 xfun_0.62 cachem_1.1.0
## [7] knitr_1.52 htmltools_0.5.9 rmarkdown_2.32
## [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_0.12.0 yaml_2.3.12
## [19] otel_0.3.0 BiocManager_1.30.27 jsonlite_2.0.0
## [22] rlang_1.3.0