GitHub - metamaden/recountmethylation: Utilities to access and analyze harmonized databases of public DNAm arrays from GEO. (original) (raw)

Authors

Sean K. Maden, Reid F. Thompson, Kasper D. Hansen, Abhinav Nellore

Overview

The recountmethylation package provides access to databases of DNA methylation (DNAm) data from over 62,000 cumulative sample records with IDATs in the Gene Expression Omnibus (GEO, available by November, 2020). Samples were run using either of 2 Illumina BeadArray platform types, either the older HM450K platform or the newer EPIC/HM850K platform. The database compilation files include mined, mapped, and model-based sample metadata, and DNAm data in the form of either raw/unnormalized red and green signals, raw/unnormalized methylated and unmethylated signals, or normalized DNAm fractions (a.k.a. "Beta-values").

Installation and data access

From an active R session, install the latest available package version from Bioconductor with:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("recountmethylation")

You may also install the package from GitHub using:

require(devtools); install_github("metamaden/recountmethylation").

See the package User's Guide vignette for more details and background about the datasets.

Manuscript

If you use recountmethylation in published work, please cite the following paper:

Sean K Maden, Reid F Thompson, Kasper D Hansen, Abhinav Nellore, 'Human methylome variation across Infinium 450K data on the Gene Expression Omnibus', NAR Genomics and Bioinformatics, Volume 3, Issue 2, June 2021, lqab025, https://doi.org/10.1093/nargab/lqab025

Package disclaimer

Please note the following disclaimer regarding the data contained in the compilation files.

Databases accessed with recountmethylation 
contain data from GEO (ncbi.nlm.nih.gov/geo/), 
a live public database where alterations to 
online records can cause discrepancies with 
stored data over time. We cannot guarantee 
the accuracy of stored data, and advise users 
cross-check their findings with latest available 
records.