Package 'GSE142512'

Title: GSE142512 DNA Methylation ExperimentHub Data
Description: Provides ExperimentHub access to processed DNA methylation resources derived from GEO accession GSE142512. The resources contain Illumina HumanMethylation450 and Infinium MethylationEPIC data represented as RangedSummarizedExperiment objects with beta, M, and CN assays, hg19 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 23:02:51 UTC
Source: https://github.com/BiocStaging/GSE142512

Help Index

GSE142512 methylation data in ExperimentHub

Description

The GSE142512 package provides ExperimentHub access to processed DNA methylation resources derived from GEO accession GSE142512.

Details

The hosted resources are RangedSummarizedExperiment objects created from Illumina HumanMethylation450 and Infinium MethylationEPIC GenomicRatioSet objects. They contain beta, M, and CN assays with hg19 genomic ranges and sample-level phenotype metadata.

The resources are hosted on Zenodo at https://zenodo.org/records/21198533 and are registered for access through ExperimentHub.

See browseVignettes("GSE142512") for usage examples.

See Also

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142512

Load GSE142512 ExperimentHub resources

Description

Convenience helpers for loading processed GSE142512 DNA methylation resources from ExperimentHub.

Usage

GSE142512(platform = c("450K", "EPIC"), metadata = FALSE)

GSE142512_GPL13534_450K(metadata = FALSE)

GSE142512_GPL21145_EPIC(metadata = FALSE)

Arguments

platform

character(1). Platform to load. Use "450K" for the GPL13534 Illumina HumanMethylation450 resource or "EPIC" for the GPL21145 Infinium MethylationEPIC resource.
metadata

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

Details

The package registers two ExperimentHub resources: GSE142512_GPL13534_450K and GSE142512_GPL21145_EPIC. Each resource contains beta, M, and CN assays with hg19 genomic ranges and sample-level phenotype metadata.

The resource-title accessors are generated from ‘inst/extdata/metadata.csv’ when the package is loaded.

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 = "GSE142512")
metadata <- utils::read.csv(metadata_file, stringsAsFactors = FALSE)
metadata[, c("Title", "Genome", "RDataClass")]

if (interactive()) {
    library(GSE142512)
    GSE142512(platform = "450K", metadata = TRUE)
    se450k <- GSE142512(platform = "450K")
    seEPIC <- GSE142512(platform = "EPIC")
    se450k
    seEPIC
}