ewas_tools: a quality control toolset for the Illumina Infinium DNA methylation platforms

The following functionality is offered for the 450K and EPIC chips:

• Screen for problematic samples, e.g. failed assays, mislabeled or contaminated samples (control_metrics, check_sex, snp_outliers).
• Compute detection p-values and mask respective data points (detectionP, mask).
• Preprocess the data (correct_dye_bias, dont_normalize).
• Estimate leukocyte composition in case of blood samples (estimateLC)

Read the vignette on the recommended QC workflow at https://hhhh5.github.io/ewastools/articles/exemplary_ewas.html.

Package documentation is available at https://hhhh5.github.io/ewastools/.

An open access paper describing the quality checks implemented in this package in detail is available at http://doi.org/10.1186/s13148-018-0504-1. A vignette demonstrating the application of quality control checks on a public dataset is provided as well.

A second paper (open access) describing the improved detection p-values implemented in ewastools can be found at https://doi.org/10.1186/s13148-019-0615-3.

For installation please run devtools::install_github("hhhh5/ewastools")