Package 'GSE280465'

Title: GSE280465 EPICv2 Methylation ExperimentHub Data
Description: Provides ExperimentHub access to a processed DNA methylation resource derived from GEO accession GSE280465. The resource contains adult Illumina Infinium MethylationEPIC version 2 data from 163 samples across four tissue types, represented as a RangedSummarizedExperiment with beta, M, and CN assays, hg38 genomic ranges, and sample phenotype metadata.
Authors: Paul Ruiz Pinto [aut, cre] (ORCID: <https://orcid.org/0009-0007-6714-3566>)
Maintainer: Paul Ruiz Pinto <[email protected]>
License: Artistic-2.0
Version: 0.99.0
Built: 2026-07-05 11:32:26 UTC
Source: https://github.com/BiocStaging/GSE280465

Help Index

GSE280465 EPICv2 methylation data in ExperimentHub

Description

The GSE280465 package provides ExperimentHub access to a processed adult DNA methylation resource derived from GEO accession GSE280465.

Details

The hosted resource is a RangedSummarizedExperiment created from an Illumina Infinium MethylationEPIC version 2 GenomicRatioSet. It contains beta, M, and CN assays for 163 adult samples from 47 individuals across buccal, saliva, dried blood spot, and peripheral blood mononuclear cell tissues.

The resource is hosted on Zenodo at https://zenodo.org/records/21200586 and is registered for access through ExperimentHub.

See browseVignettes("GSE280465") for a usage example.

See Also

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE280465

Load the GSE280465 ExperimentHub resource

Description

Convenience helper for loading the GSE280465 EPICv2 adult cross-tissue DNA methylation resource from ExperimentHub.

Usage

GSE280465(metadata = FALSE, filterBy = "GSE280465_GPL33022_EPICv2")

GSE280465_GPL33022_EPICv2(metadata = FALSE)

Arguments

metadata

logical(1). If TRUE, return ExperimentHub metadata for the matching resource. If FALSE, load the matching resource.
filterBy

character(1). Resource title used to filter the ExperimentHub entries for this package.

Details

The resource is registered as GSE280465_GPL33022_EPICv2 in ExperimentHub. It contains beta, M, and CN assays with hg38 genomic ranges and sample-level phenotype metadata.

The GSE280465_GPL33022_EPICv2() function is the resource-title accessor generated from ‘inst/extdata/metadata.csv’ when the package is loaded. It returns the same hosted resource as GSE280465().

Value

When metadata = FALSE, a RangedSummarizedExperiment. When metadata = TRUE, the matching ExperimentHub metadata.

See Also

ExperimentHub, listResources, loadResources

Examples

metadata_file <- system.file("extdata", "metadata.csv", package = "GSE280465")
metadata <- utils::read.csv(metadata_file, stringsAsFactors = FALSE)
metadata[, c("Title", "Genome", "RDataClass")]

if (interactive()) {
    library(GSE280465)
    GSE280465(metadata = TRUE)
    se <- GSE280465()
    se
    se <- GSE280465_GPL33022_EPICv2()
}